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NOTICE! This is a static HTML version of the legacy LOCI Software Trac.

LOCI projects are now located on GitHub. The Bio-Formats project can be found here.

Ticket Summary Owner Type Status Priority Milestone Component Severity Resolution
#1 Leica Reader openBytes() Exception somebody defect closed minor bio-formats fixed
#2 Bio-Formats Importer plugin loses some channels when merging melissa defect closed minor plugins fixed
#3 Support for Volocity databases melissa enhancement closed minor bio-formats duplicate
#4 Bio-Formats native solution curtis task closed critical bio-formats fatal fixed
#5 Better channel merging in Bio-Formats Importer melissa enhancement closed minor plugins non-issue fixed
#6 Improve VisBio.exe Windows launcher curtis enhancement closed trivial visbio3.50 visbio serious moved
#7 Investigate source code auto-formatting tools curtis task closed trivial build serious wontfix
#8 Improve Checkstyle configuration to enforce additional coding standards curtis enhancement closed trivial build serious moved
#9 Improve selection of overlays sorber enhancement closed minor visbio fixed
#10 Export overlay statistics to .xls sorber enhancement closed major visbio fixed
#11 Improve behavior on multi-head configurations curtis enhancement closed trivial visbio4.0 visbio serious moved
#12 Override createSubtitle() properly curtis defect closed trivial browser minor fixed
#13 Behavior of overlay tools when no data object present curtis defect closed minor visbio3.40 visbio fixed
#14 Format handler subclasses should send status update events melissa enhancement closed minor bio-formats fixed
#15 Base TransientSelectBox resizing on pixel and not domain coordinates sorber defect closed trivial visbio fixed
#16 OME Uploader API should be merged with format writer logic melissa task closed minor bio-formats fixed
#17 Bio-Formats importer does not set calibration information for alternate window types curtis defect closed major plugins major fixed
#18 Support for additional dimensions (wrapped into channel) curtis enhancement closed major bio-formats fixed
#19 File pattern detection sometimes depends on the file chosen as the basis curtis defect closed minor bio-formats serious fixed
#20 Use QTObject.dispose() in QTJava-related code to avoid potential crashes and memory leaks melissa task closed trivial bio-formats fixed
#21 Residuals colorization is inconsistent nor defect closed trivial slim-plotter serious moved
#22 Data colorization is inconsistent curtis defect closed minor slim-plotter fixed
#23 Minimum and maximum color value sliders do not work as expected nor defect closed minor slim-plotter serious fixed
#24 Multiple exponential curve fitting nor enhancement closed critical slim-plotter critical fixed
#25 Log scale improvements curtis enhancement closed minor slim-plotter fixed
#26 Finish interactive color scale features curtis enhancement closed major slim-plotter fixed
#27 Write to SDT format curtis enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#28 Ability to bin channels together and export to SDT nor enhancement closed major slim-plotter serious moved
#29 Zeiss LSM/MDB bug: "No such method: mdb_open" melissa defect closed major bio-formats fixed
#30 State logic needs support for invertible operations curtis enhancement closed critical visbio3.50 visbio serious moved
#31 Save/restore state feature is broken curtis defect closed critical visbio3.50 visbio serious moved
#32 Java2D support is broken curtis defect closed major visbio wontfix
#33 16-bit images do not display properly curtis defect closed critical visbio4.0 visbio fixed
#34 Better ImageFlatField support within VisAD curtis enhancement closed blocker visbio4.0 visbio serious moved
#35 More intelligent usage of Bio-Formats curtis enhancement closed critical visbio4.0 visbio fatal moved
#36 4-channel data does not import correctly curtis defect closed major visbio3.40 visbio fixed
#37 Resampling should not call unpackFloats curtis defect closed critical visbio4.0 visbio serious moved
#38 Arbitrary slicing does not work for large data curtis defect closed critical visbio3.40 visbio fixed
#39 Dimension labels cannot be overridden curtis defect closed critical visbio3.40 visbio serious moved
#40 AVI writer produces incorrect video files melissa defect closed minor bio-formats fixed
#41 QuickTime reader colors for mjpb-encoded data differ from QTJava results melissa defect closed minor bio-formats fixed
#42 Support for QuickTime Sorenson 3 codec melissa enhancement closed trivial bio-formats fixed
#43 Some QuickTime movies erroneously report missing resource fork melissa defect closed minor bio-formats fixed
#44 Support for AVI msrle codec melissa enhancement closed trivial bio-formats fixed
#45 Support for QuickTime rpza codec melissa enhancement closed trivial bio-formats fixed
#46 Thumbnailing support should use Bio-Formats curtis enhancement closed critical visbio4.0 visbio serious moved
#47 Microns per pixel support is broken curtis defect closed critical visbio fixed
#48 Eliminate "range component" concept from VisBio curtis enhancement closed critical visbio4.0 visbio serious moved
#49 More flexible cache manager curtis enhancement closed critical visbio4.0 visbio serious moved
#50 TIFF export should write in OME-TIFF format curtis enhancement closed major visbio3.50 visbio serious moved
#51 Support for multi-series data curtis enhancement closed major visbio4.0 visbio serious moved
#52 Revamp GUI for next major release curtis enhancement closed major visbio4.0 visbio serious moved
#53 OME download feature should use ImageFlatField curtis enhancement closed major visbio4.0 visbio serious moved
#54 Screencasts for LOCI software tools curtis task closed trivial docs non-issue invalid
#55 Support for Volocity format melissa enhancement closed major bio-formats-5.0 bio-formats serious fixed
#56 Support for compressed QuickTime headers melissa enhancement closed minor bio-formats fixed
#57 Execute ImageJ macros on virtual stacks melissa enhancement closed minor plugins major fixed
#58 Update OME plugin for ImageJ web site curtis task closed major docs non-issue fixed
#59 Create OME Notes web page curtis task closed major docs non-issue fixed
#60 Quality of exponential curve fit is questionable nor defect closed critical slim-plotter serious moved
#61 Integrate Slim Plotter features into VisBio curtis task closed minor visbio5.0 visbio serious moved
#62 Record proprietary metadata under Image>CustomAttributes in OME-XML melissa enhancement closed minor bio-formats fixed
#63 Gray out File>Save and QuickSave when appropriate curtis defect closed major notes wontfix
#64 Automatically create 2D display with overlays sorber enhancement closed minor visbio fixed
#65 Cache indicators can report erroneous caching situation curtis defect closed major browser fatal fixed
#66 Set default overlays filename curtis enhancement closed minor visbio3.40 visbio fixed
#67 Finish OME-TIFF and Bio-Formats section of FAQ web page curtis task closed major docs non-issue fixed
#68 Test all format readers with omebf melissa task closed critical bio-formats fatal fixed
#69 Adapt Data Converter into a Bio-Formats export GUI component curtis task closed critical bio-formats non-issue wontfix
#70 Additional OME-TIFF sample data curtis task closed critical docs non-issue fixed
#71 Use OME Notes for metadata viewing and editing curtis enhancement closed critical visbio4.0 visbio serious moved
#72 More powerful template engine melissa task closed critical notes non-issue wontfix
#73 Graphical template editor melissa task closed critical notes non-issue wontfix
#74 Leverage the template engine across several distinct use cases melissa task closed critical notes non-issue wontfix
#75 Improve robustness of OME Web Start launcher curtis defect closed critical visbio3.50 visbio serious moved
#76 011B1_Morph_A01_s1_w1.TIF fails to import into OME using Bio-Formats melissa defect closed major bio-formats fixed
#77 Some TIFF comment key/value pairs are parsed incorrectly melissa enhancement closed minor bio-formats fixed
#78 Implement OMERO upload and download logic curtis task closed critical ome-io non-issue fixed
#79 Image window does not size down properly after being sized up curtis defect closed minor browser fixed
#80 Update OME-TIFF web site to reflect proposed modifications curtis task closed critical docs non-issue fixed
#81 More OME-TIFF code examples curtis task closed major docs non-issue duplicate
#82 Better support for writing OME-TIFF, including proposed modifications curtis enhancement closed critical bio-formats major fixed
#83 ArrayIndexOutOfBoundsException in TIFF metadata parsing melissa defect closed major bio-formats fixed
#84 Use system response file to calibrate data via deconvolution nor enhancement closed critical slim-plotter serious moved
#85 Look into other curve fitting algorithms nor task closed trivial slim-plotter serious fixed
#86 Implement spectral projection feature nor enhancement closed minor slim-plotter serious moved
#87 Exporter plugin doesn't preserve pixel type melissa defect closed major plugins fixed
#88 Need system to scale selection areas to pixel coordinates sorber defect closed critical visbio fixed
#89 Update Polyline length as mouse is dragged sorber enhancement closed trivial visbio fixed
#90 Format and organize API methods in OverlayObject and subclasses sorber defect closed trivial visbio fixed
#91 IPLabReader fails to populate OME-XML metadata store melissa defect closed major bio-formats fixed
#92 Notebook crashes when given a file from the command line melissa defect closed critical notes fixed
#93 Move IFormatReader.swapDimensions into separate DimensionSwapper delegate melissa enhancement closed major bio-formats fixed
#94 Eliminate IFormatHandler's ubiquitous "String id" parameter melissa task closed critical bio-formats fixed
#95 Rename IFormatWriter.save to IFormatWriter.saveImage melissa task closed trivial bio-formats fixed
#96 Investigate TestNG data-driven testing melissa task closed minor bio-formats fixed
#97 Fix Leica color channel handling melissa defect closed critical bio-formats fixed
#98 Add ability to toggle metadata collection melissa enhancement closed major bio-formats fixed
#99 Remove "ignore color lookup table" option melissa task closed minor plugins fixed
#100 Investigate ways to minimize VisAD's dependencies on Bio-Formats packages curtis task closed major bio-formats fixed
#101 Look into existing electronic notebooks melissa task closed critical notes non-issue wontfix
#102 OverlayNodedObject getData() method sometimes makes invalid Gridded2DSets sorber defect closed major visbio fixed
#103 Exception when removing display curtis defect closed minor visbio3.50 visbio serious moved
#104 Polyline getData() sometimes breaks when filled box is checked sorber defect closed major visbio fixed
#105 Add rotation buttons to DisplayControls for 2D displays sorber enhancement closed minor visbio fixed
#106 make working with large data objects more efficient curtis enhancement closed major visbio4.0 visbio serious moved
#107 QuickTime mjpb files no longer work melissa defect closed critical bio-formats fixed
#108 Investigate composite image stacks in ImageJ melissa enhancement closed minor plugins fixed
#109 OverlayArrow getData breaks for zero-length arrows sorber defect closed trivial visbio fixed
#110 Make invisible overlay objects automatically delete themselves sorber defect closed major visbio worksforme
#111 Better data transform changed events curtis defect closed major visbio3.50 visbio serious moved
#112 Support for NRRD format melissa enhancement closed minor bio-formats fixed
#113 Min/max calculation is incorrect for byte arrays melissa defect closed critical bio-formats fixed
#114 Bio-Formats cannot handle files larger than 2GB melissa defect closed critical bio-formats fixed
#115 Arbitrary slicing can throw NullPointerException curtis defect closed critical visbio3.40 visbio fixed
#116 Add Dr. Inman's smoothing procedure to FreeformTool sorber enhancement closed major visbio fixed
#117 Eliminate invalid characters in generated OME-XML melissa defect closed major bio-formats fixed
#118 Support for MetaMorph .ND files melissa enhancement closed minor bio-formats fixed
#119 Make sure Polyline and Freeform tools are in good working order sorber task closed critical visbio fixed
#120 Modify visad.util.CursorUtil to work robustly with coordinates of size 2 or 3 curtis defect closed major visbio3.50 visbio serious moved
#121 Support for externally compressed files melissa enhancement closed minor bio-formats fixed
#122 OverlayMarker size should scale with zoom curtis defect closed major visbio3.50 visbio serious moved
#123 Enable erasing of freeform just drawn sorber defect closed major visbio fixed
#124 Use more powerful erasing algorithm in FreeformTool sorber defect closed critical visbio fixed
#125 Automatically launch spreadsheet application when exporting overlays sorber enhancement closed critical visbio fixed
#126 Investigate leveraging existing ontology/terminology solutions melissa task closed major notes non-issue wontfix
#127 Upload to OME plugin does not respect Cancel button melissa defect closed minor plugins fixed
#128 Support for BioRad companion files melissa enhancement closed minor bio-formats fixed
#129 Fix how data browser handles OME images melissa defect closed major browser fixed
#130 Colorize data in intensity pane according to lifetime values nor enhancement closed minor slim-plotter major fixed
#131 Additional constructors melissa enhancement closed major notes fixed
#132 Write a tutorial for making measurements in VisBio sorber task closed major visbio fixed
#133 StatsOptionsPane appears in "Load overlays..." file chooser sorber defect closed critical visbio fixed
#134 Align peaks needs to be more configurable nor enhancement closed major slim-plotter serious moved
#135 Support for spectral calibration nor enhancement closed critical slim-plotter serious moved
#136 Add pixel value check to testing framework melissa enhancement closed major bio-formats fixed
#137 FITS and PGM do not work with compressed data melissa defect closed trivial bio-formats fixed
#138 Document details of supported formats melissa task closed minor bio-formats non-issue fixed
#139 Clean up VisBio noded overlays code sorber task closed critical visbio fixed
#140 Consolidate error message display methods in OverlayIO and OverlayWidget curtis task closed minor visbio3.50 visbio serious moved
#141 Decide where instance of SpreadsheetLauncher should live sorber task closed critical visbio wontfix
#142 Update JGoodies Looks jar to include LookUtils (for determining OS type). sorber defect closed critical visbio fixed
#143 Enhance EPS support melissa defect closed minor bio-formats wontfix
#144 Fix >2GB ND2 files melissa defect closed major bio-formats fixed
#145 Add rough check to improve speed of freeform erasing curtis enhancement closed minor visbio3.50 visbio serious moved
#146 Prevent ONOs from containing consecutive colocational nodes sorber defect closed critical visbio fixed
#147 Polyline array out of bounds exception. sorber defect closed critical visbio fixed
#148 Do something about large quantities of metadata melissa defect closed critical bio-formats fixed
#149 Turn off statistics updating when drawing a FreeformExtension curtis defect closed minor visbio3.50 visbio serious moved
#150 Assorted peculiar VisBio exceptions curtis defect closed minor visbio3.40 visbio worksforme
#151 Multi-series Slidebook support melissa defect closed major bio-formats fixed
#152 Remove Swing components from OME plugin melissa defect closed major plugins fixed
#153 Parse metadata in Leica TCS TIFFs melissa enhancement closed major bio-formats fixed
#154 NullPointerException when populating template fields melissa defect closed major notes fixed
#155 PixelSizeT disappears melissa defect closed critical bio-formats fixed
#156 Investigate LOCI Java software development in Eclipse curtis task closed minor build minor fixed
#157 More Bio-Formats sample data in various formats melissa task closed minor docs serious fixed
#158 Add support for BigTiff melissa enhancement closed minor bio-formats fixed
#159 Add support for compressed ZVI images melissa enhancement closed minor bio-formats fixed
#160 Clean up overlays tutorial curtis task closed trivial visbio3.40 visbio fixed
#161 Make volume rendering checkbox friendlier to use curtis enhancement closed minor visbio3.40 visbio fixed
#162 GUI usability improvements curtis enhancement closed minor visbio3.50 visbio serious moved
#163 Expand VisBio as a toolkit with scriptable components curtis enhancement closed critical visbio5.0 visbio serious moved
#164 Emissions spectrum view in 2D pane nor enhancement closed minor slim-plotter serious moved
#165 Another arbitrary slicing NullPointerException curtis defect closed critical visbio3.40 visbio fixed
#166 LegacyQTReader is broken melissa defect closed major bio-formats fixed
#167 Motion JPEG-B support for single-image QuickTime movies is broken melissa defect closed trivial bio-formats fixed
#168 LegacyQTWriter is broken melissa defect closed major bio-formats fixed
#169 LegacyQTWriter cannot save using Motion JPEG-B codec melissa defect closed trivial bio-formats fixed
#170 Investigate ImageJ's VirtualStack objects melissa task closed trivial bio-formats fixed
#171 Improve OME-TIFF grouping logic curtis enhancement closed critical bio-formats fixed
#172 Better usage of JAI Image I/O Tools melissa task closed minor bio-formats fixed
#173 Standard way to "fail through" to another reader melissa task closed minor bio-formats minor wontfix
#174 Investigate usage of Sanselan image library melissa task closed trivial bio-formats fatal fixed
#175 More cohesive floating point image support melissa enhancement closed major bio-formats fixed
#176 ImageJ stack ordering broken melissa defect closed major plugins fixed
#177 Additional plugin options melissa enhancement closed minor plugins major fixed
#178 Add support for Imaris 5.5 melissa enhancement closed major bio-formats non-issue fixed
#179 Add support for compressed LIM files melissa enhancement closed minor bio-formats-5.0 bio-formats serious fixed
#180 AVI codecs supported by NIS Elements melissa enhancement closed trivial bio-formats fixed
#181 Investigate LSM data with nonstandard LZW compression melissa task closed minor bio-formats serious fixed
#182 Fix bug with >2GB LIF files melissa defect closed major bio-formats fixed
#183 Devise a scheme to embed calibration information into the SDT format nor task closed major slim-plotter serious moved
#184 Additional logic for handling background issues nor enhancement closed major slim-plotter serious moved
#185 Plot system response data graphically nor enhancement closed major slim-plotter serious moved
#186 Plot chi-squared error graphically nor enhancement closed major slim-plotter serious moved
#187 Model some data for testing nor task closed major slim-plotter serious fixed
#188 Overlapping line and surface plots nor enhancement closed minor slim-plotter serious moved
#189 Save/export to figure file nor enhancement closed minor slim-plotter serious moved
#190 Export to spreadsheet nor enhancement closed minor slim-plotter serious moved
#191 3-view nor enhancement closed minor slim-plotter serious moved
#192 Default implementation for saveBytes melissa enhancement closed minor bio-formats fixed
#193 Test omeul with OME 2.6.1 melissa task closed minor bio-formats fatal fixed
#194 Investigate usage of JMF library melissa task closed trivial bio-formats fixed
#195 Cannot construct 2-channel images with ImageTools melissa defect closed major bio-formats fixed
#196 ZVI reader sometimes reverses Z and T dimensions melissa defect closed major bio-formats fixed
#197 Bio-Formats Importer fails with indexed images melissa defect closed critical plugins fixed
#198 OME-TIFF files fail with Bio-Formats Importer plugin melissa defect closed critical bio-formats fixed
#199 Fix exception with new OIB files melissa defect closed critical bio-formats fatal fixed
#200 Split channels option divides image planes across the wrong dimension when specifying ranges melissa defect closed major plugins fatal fixed
#201 Improve configuration file generator melissa enhancement closed major bio-formats fatal fixed
#202 Create "Bio-Formats Stack Splitter" plugin curtis task closed major bio-formats fatal fixed
#203 Some PICT files have incorrect pixel type melissa defect closed major bio-formats fixed
#204 Support lossless JPEG in DICOM reader melissa enhancement closed major bio-formats minor fixed
#205 Window titles can become too long melissa defect closed minor plugins serious fixed
#206 Color merge throws an exception melissa defect closed major plugins major fixed
#207 Slicer plugin throws an exception when there is no active image melissa defect closed minor plugins minor fixed
#208 Add information about format versions to web site melissa task closed minor docs non-issue fixed
#209 OME download is broken curtis defect closed major visbio3.40 visbio critical fixed
#210 Better file stitching in BioradReader melissa enhancement closed major bio-formats non-issue fixed
#211 Add ImageJ plugin that merges/colorizes channels melissa enhancement closed minor plugins non-issue fixed
#212 Reading OME-TIFF file with '-nometa' throws exception melissa defect closed major bio-formats serious fixed
#213 OMETiffReader should parse OriginalMetadata melissa defect closed minor bio-formats minor fixed
#214 Add support for InCell1000 HCS format melissa enhancement closed major bio-formats non-issue fixed
#215 Stack Slicer window titles must be distinct melissa defect closed minor plugins major fixed
#216 Improve window titles for multi-file datasets melissa enhancement closed trivial plugins cosmetic fixed
#217 Write alternate ND2 reader using Nikon SDK melissa enhancement closed major bio-formats non-issue fixed
#218 Fix memory issue with OLE-based formats melissa defect closed critical bio-formats major fixed
#219 Some Slidebook files have incorrect dimensions melissa defect closed major bio-formats major fixed
#220 LZW decoder misbehaves for some LZW-compressed TIFFs melissa defect closed major bio-formats major fixed
#221 Add support for Olympus APL file format melissa enhancement closed major bio-formats non-issue fixed
#222 SDT reader should fully parse SETUP metadata block melissa enhancement closed minor bio-formats non-issue fixed
#223 Make Exporter work with 48-bit RGB data melissa defect closed major plugins serious fixed
#224 Display metadata in image info window melissa enhancement closed major plugins non-issue fixed
#225 Hyperstack option for "View stack with" melissa task closed major plugins non-issue fixed
#226 "Use virtual stack" option for Bio-Formats Importer melissa enhancement closed major plugins non-issue fixed
#227 Can't save metadata in ImageJ melissa defect closed major plugins serious fixed
#228 Add support for writing BigTIFF files melissa enhancement closed major bio-formats minor fixed
#229 Support multi-series OME-TIFF export melissa defect closed major bio-formats serious fixed
#230 Support for sub-channels in ImageJ melissa enhancement closed major plugins cosmetic fixed
#231 Improve bfconvert melissa enhancement closed major bio-formats-4.1 bio-formats serious fixed
#232 Fix TIFF performance issues melissa defect closed critical bio-formats critical invalid
#233 Improve time performance of subimage methods melissa enhancement closed trivial bio-formats minor fixed
#234 Bio-Formats Importer plugin problems when cropping multiple series melissa defect closed major plugins major fixed
#235 Add support for new Metamorph format melissa enhancement closed major bio-formats non-issue fixed
#236 QuickTime resource fork parsing on Mac file systems throws ArithmeticException melissa defect closed critical bio-formats critical fixed
#237 Image planes from LegacyQTReader can no longer be displayed melissa defect closed critical bio-formats critical fixed
#238 Exception is thrown when multiple BioRad datasets are in the same directory melissa defect closed minor bio-formats serious fixed
#239 ArrayIndexOutOfBoundsException for IndexedColorModel and/or DICOM melissa defect closed minor bio-formats serious fixed
#240 Update OMEROReader to work with 2.3 server melissa defect closed critical bio-formats major fixed
#241 More robust channel assignment melissa defect closed major bio-formats minor fixed
#242 Turn off NetCDF debugging output melissa task closed major bio-formats critical fixed
#243 Thumbnail pixel values are incorrect melissa defect closed major bio-formats major fixed
#244 NullPointerException in GatanReader melissa defect closed major bio-formats fatal fixed
#245 FV1000 reader dies when analyzing Bio-Rad ROIs melissa defect closed major bio-formats fatal fixed
#246 Bio-Rad data.raw files are not recognized melissa defect closed major bio-formats major fixed
#247 Sequential setId calls with SVSReader can throw an exception melissa defect closed critical bio-formats critical fixed
#248 MetamorphTiffReader.isThisType throws NullPointerException on some files melissa defect closed critical bio-formats fatal fixed
#249 Sequential setId calls with BioRadReader do not fully reset state melissa defect closed critical bio-formats critical fixed
#250 Bio-Rad reader throws StringIndexOutOfBoundsException with some XML fragments melissa defect closed critical bio-formats fatal fixed
#251 Bio-Rad reader sometimes looks for an incorrectly named PIC file melissa defect closed major bio-formats serious fixed
#252 Bio-Rad reader does not include data.raw files on its used files list melissa defect closed minor bio-formats minor fixed
#253 BioRad reader doesn't support lookup tables melissa enhancement closed minor bio-formats non-issue fixed
#254 FV1000 reader doesn't support lookup tables melissa enhancement closed minor bio-formats non-issue fixed
#255 ICS reader performs poorly with highly multichannel ICS datasets melissa defect closed major bio-formats serious fixed
#256 Add new isThisType signature melissa enhancement closed minor bio-formats non-issue fixed
#257 Improve RAUrl melissa defect closed minor bio-formats-4.1 bio-formats minor fixed
#258 Move Zip detection logic to ZipReader melissa enhancement closed minor bio-formats-4.1 bio-formats non-issue fixed
#259 Add support for JPEG2000-compressed SVS files melissa enhancement closed major bio-formats non-issue fixed
#260 omeul doesn't upload original file(s) melissa defect closed major bio-formats minor fixed
#261 omeul should upload OME-XML metadata melissa defect closed major bio-formats serious fixed
#262 Readd configurable caching support to Data Browser using Bio-Formats caching package curtis enhancement closed critical plugins serious fixed
#263 Bio-Formats configuration dialog curtis task closed major plugins serious fixed
#264 Better ImageJ open/save integration curtis enhancement closed major plugins non-issue wontfix
#265 Separate widget for each sub-C dimension melissa enhancement closed minor plugins non-issue fixed
#266 L2D datasets cannot be imported using omebf melissa defect closed minor bio-formats serious wontfix
#267 Write ImageJ plugin to swap dimension labels melissa task closed major plugins non-issue fixed
#268 OMEWriter does not save all metadata melissa defect closed major bio-formats serious duplicate
#269 OMEReader does not read all metadata melissa defect closed major bio-formats serious fixed
#270 Thumbnail generation fails with some MNG files melissa defect closed major bio-formats serious fixed
#271 Some MNG datasets have pixel type mismatch melissa defect closed minor bio-formats serious fixed
#272 Ability to explicitly disable file stitching for certain files melissa defect closed major bio-formats-4.3 test-suite serious fixed
#273 Some readers do not have sane file type checking melissa defect closed major bio-formats serious fixed
#274 Add animate key to ImageViewer melissa enhancement closed trivial bio-formats non-issue fixed
#275 Review importer options curtis task closed major plugins minor fixed
#276 Make ND2 reader faster melissa enhancement closed minor bio-formats minor fixed
#277 Bio-Formats drag and drop window curtis task closed minor plugins non-issue fixed
#278 Move OME/OMERO plugins out of loci_tools.jar curtis task closed critical build minor fixed
#279 Add support for FEI SEM format melissa enhancement closed minor bio-formats non-issue fixed
#280 Move ImageJ-specific logic out of OMEUtils melissa defect closed major bio-formats minor fixed
#281 Attempting to colorize single channel data throws an exception melissa defect closed major plugins serious fixed
#282 Slidebook image names are truncated melissa defect closed major bio-formats minor fixed
#283 OMERO download has strange CLASSPATH requirements melissa defect closed critical plugins critical fixed
#284 ZVI reader ignores xy positions beyond the first melissa defect closed major bio-formats serious fixed
#285 LSM timestamps not reliably parsed melissa defect closed major bio-formats serious fixed
#286 Investigate improving AVI support based on new AVI_Reader melissa task closed major bio-formats serious fixed
#287 SimplePCI reader fails to parse dimensional parameters for some CXDs melissa defect closed major bio-formats serious fixed
#288 Animated GIF reader sometimes leaves "trails" melissa defect closed major bio-formats serious fixed
#289 Review and adjust ImageJ color-related options curtis task closed critical bio-formats-4.2 plugins major fixed
#290 Util.openProcessor does not properly handle RGB data melissa defect closed major plugins serious fixed
#291 Some DICOM files throw ArrayIndexOutOfBounds melissa defect closed major bio-formats serious fixed
#292 SDT file possibly has wrong channel count melissa defect closed major bio-formats serious duplicate
#293 SDT file possibly has wrong channel count melissa defect closed major bio-formats serious fixed
#294 Add support for Aquacosmos .naf format melissa enhancement closed minor bio-formats-5.0 bio-formats non-issue fixed
#295 Better support for renamed Leica files melissa defect closed major bio-formats serious fixed
#296 Stitching multiple series needs improvement melissa defect closed minor bio-formats-4.2.1 bio-formats serious fixed
#297 Add support for Patch-Master electrophysiology files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#298 SPW changes break Flex reader curtis defect closed major bio-formats serious fixed
#299 Parse picture names from Openlab LIFF files melissa enhancement closed minor bio-formats serious fixed
#300 ZVI reader throws ArrayIndexOutOfBoundsException melissa defect closed major bio-formats serious fixed
#301 Exception thrown when colorizing images in ImageJ on OS X melissa defect closed major plugins serious fixed
#302 Add support for datasets produced by Vevo 770 melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#303 Add support for animated PNGs melissa enhancement closed minor bio-formats non-issue fixed
#304 Create documentation on using Bio-Formats with Ice curtis task closed critical docs critical fixed
#305 Handle mixed OME/non-OME XML blocks melissa enhancement closed minor bio-formats serious fixed
#306 Min/max threshold for region of interest nor enhancement closed minor slim-plotter non-issue moved
#307 Split IndexedColorModel into Index16ColorModel and Index32ColorModel melissa task closed minor bio-formats cosmetic fixed
#308 Sort data repository into different categories melissa task closed critical bio-formats-4.3 test-suite serious fixed
#309 Document supported metadata fields in each format curtis task closed critical docs non-issue fixed
#310 Overhaul Bio-Formats Importer curtis enhancement closed critical bio-formats-4.2 plugins serious fixed
#311 Split build into multiple components curtis task closed critical build non-issue fixed
#312 Improve TillVision support melissa enhancement closed minor bio-formats non-issue fixed
#313 Improve Slidebook metadata melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#314 Add support for vector data in PS/EPS files melissa enhancement closed minor bio-formats-5.0 bio-formats minor fixed
#315 Investigate how to handle ROIs and overlays within proprietary file formats melissa enhancement closed major bio-formats-4.1 bio-formats non-issue fixed
#316 Investigate using non-custom type for BufferedImages melissa task closed major bio-formats serious fixed
#317 Add file format extension filter to Bio-Formats Exporter curtis enhancement closed minor plugins serious fixed
#318 Improve Nikon NEF support melissa enhancement closed major bio-formats serious fixed
#319 Speed up Slidebook reading melissa task closed major bio-formats minor fixed
#320 Fix compressed 16-bit Flex files melissa defect closed major bio-formats critical fixed
#321 Investigate adding FindBugs targets curtis task closed trivial build non-issue fixed
#322 Eliminate native library dependencies melissa task closed critical bio-formats serious fixed
#323 Add support for writing JPEG2000 melissa enhancement closed minor bio-formats non-issue fixed
#324 Add support for Minolta MRW format melissa enhancement closed major bio-formats non-issue fixed
#325 More flexible window naming curtis enhancement closed minor plugins serious fixed
#326 Allow "merge to RGB" and "split channels" options to be used simultaneously melissa enhancement closed minor bio-formats-4.2 plugins serious invalid
#327 Allow ImageJ plugin to check for updates melissa enhancement closed major bio-formats-4.0 plugins non-issue fixed
#328 Parse time interval tag in IPLab files melissa defect closed major bio-formats serious fixed
#329 Exception when saving from Image5D window melissa defect closed major plugins serious fixed
#330 Cannot read OME-TIFF files saved from Image5D window melissa defect closed major plugins serious fixed
#331 Fix FV1000 reader to handle OIF version 2 melissa defect closed major bio-formats serious fixed
#332 Report field count for multifield data melissa enhancement closed major bio-formats-4.0 bio-formats serious fixed
#333 Decide how to handle XZ and XT scans melissa task closed major bio-formats-4.1 bio-formats serious fixed
#334 Parse instrument metadata from MicroManager files melissa enhancement closed major bio-formats-4.0 bio-formats serious fixed
#335 Fix AVIs produced by OpenBox melissa defect closed major bio-formats serious fixed
#336 Add support for MPEG-2/.vob files melissa enhancement closed minor bio-formats non-issue fixed
#337 Consider expanding "Colorize Channels" option melissa enhancement closed major bio-formats-4.0 plugins non-issue fixed
#338 Metadata completeness - Nikon ND2 melissa task closed major bio-formats-4.0 bio-formats serious fixed
#339 Metadata completeness - Metamorph STK melissa task closed major bio-formats-4.0 bio-formats serious fixed
#340 Metadata completeness - Leica LEI/LIF melissa task closed major bio-formats-4.0 bio-formats serious fixed
#341 Add unit tests for writers melissa enhancement closed minor bio-formats-4.0 test-suite non-issue fixed
#342 Add support for reading/writing multi-page EPS files melissa defect closed major bio-formats-4.1 bio-formats serious invalid
#343 Fix OME-XML population bugs in FV1000 reader melissa defect closed critical bio-formats-4.0 bio-formats serious fixed
#344 More robust support for 1, 2 and 4 bit images melissa enhancement closed major bio-formats minor fixed
#345 Investigate ND2 timestamp bug melissa task closed major bio-formats-4.0 bio-formats minor fixed
#346 ND2Reader reports incorrect dimensions melissa defect closed critical bio-formats-4.0 bio-formats critical fixed
#347 Better handling of OME-TIFFs without .ome.tiff extension melissa enhancement closed major bio-formats-4.1 bio-formats non-issue fixed
#348 TiffTools should return individual image tiles melissa task closed minor bio-formats-4.1 bio-formats non-issue fixed
#349 Fix known OME-XML validation errors melissa defect closed major bio-formats serious fixed
#350 Add support for IPLab-Mac file format melissa task closed major bio-formats-4.1 bio-formats non-issue fixed
#351 Metadata completeness - InCell 1000 melissa task closed major bio-formats-4.0 bio-formats minor fixed
#352 Add support for NIfTI format melissa enhancement closed minor bio-formats-4.1 bio-formats non-issue fixed
#353 Vector .psd files not supported melissa enhancement closed minor bio-formats-5.0 bio-formats serious fixed
#354 Bio-Formats writers should use the loci.common I/O classes melissa enhancement closed minor bio-formats-4.1 bio-formats serious fixed
#355 Data Browser displays time series data incorrectly melissa defect closed major bio-formats-4.0 plugins serious fixed
#356 Add support for Analyze 7.5 format melissa enhancement closed minor bio-formats-4.1 bio-formats non-issue fixed
#357 Some TIFFs cannot be read melissa defect closed critical bio-formats-4.0 bio-formats major fixed
#358 Investigate JHOVE for file format recognition curtis enhancement closed trivial bio-formats non-issue fixed
#359 Exception when reading signed 16 bit images curtis defect closed major bio-formats major fixed
#360 J2K files not supported melissa defect closed major bio-formats-4.1 bio-formats minor fixed
#361 Move JPEG-2000 logic into its' own reader melissa task closed minor bio-formats-4.1 bio-formats non-issue fixed
#362 Clean up delegation to legacy readers melissa task closed minor bio-formats-4.1 bio-formats non-issue fixed
#363 AWTImageTools.openImage misrepresents negative pixel values for int16 melissa defect closed major bio-formats-4.1 bio-formats major fixed
#364 Group DICOM files using the 'Instance Number' tag melissa enhancement closed minor bio-formats-4.1 bio-formats non-issue fixed
#365 Error parsing MDB database files: exception in mdb_fetch_row melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#366 LSM reader should accept files with .mdb extension melissa enhancement closed minor bio-formats-4.1 bio-formats serious fixed
#367 NativeND2Reader does not read Z steps correctly melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#368 Cannot read converted OME-TIFF files with JPEG-2000 compression melissa defect closed minor bio-formats-4.1 bio-formats major fixed
#369 Some tiled ZVIs throw an exception melissa defect closed major bio-formats-4.1 bio-formats major fixed
#370 Add support for lossless-compressed ZVIs melissa enhancement closed major bio-formats-4.1 bio-formats minor fixed
#371 ICS reader does not accurately report signed 16-bit data melissa defect closed major bio-formats-4.1 bio-formats major fixed
#372 MetamorphReader does not accurately search for constituent files melissa defect closed critical bio-formats-4.1 bio-formats major fixed
#373 Writers do not preserve color lookup tables melissa defect closed major bio-formats-4.1 bio-formats minor fixed
#374 Cannot construct int8 BufferedImages melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#375 Cannot construct uint32 BufferedImages melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#376 Add support for writing lossless JPEGs melissa enhancement closed minor bio-formats-5.0 bio-formats non-issue fixed
#377 Some formats take a long time to initialize melissa task closed major bio-formats-4.2 bio-formats major fixed
#378 Change bfconvert to open/save byte arrays melissa task closed major bio-formats-4.1 bio-formats major fixed
#379 EOFException reading some LEI datasets melissa defect closed major bio-formats serious fixed
#380 Error converting some LEI files to OME-TIFF melissa defect closed major bio-formats serious fixed
#381 Channel discrepancy when converting from indexed true color to OME-TIFF melissa defect closed major bio-formats serious fixed
#382 Generated OME-TIFF files have invalid UUID elements melissa defect closed major bio-formats serious fixed
#383 Generated OME-TIFF files have elements in the wrong order curtis defect closed major bio-formats-4.2 bio-formats serious fixed
#384 Generated OME-XML should use proper namespaces where appropriate curtis defect closed major bio-formats-4.2 bio-formats serious fixed
#385 Generated OME-XML has an invalid DisplayOptions element melissa defect closed major bio-formats serious fixed
#386 Add support for Leica OME data melissa task closed major bio-formats-5.0 bio-formats non-issue fixed
#387 Behavior when overcropping is inconsistent melissa defect closed trivial bio-formats-4.1 bio-formats minor fixed
#388 Flex file metadata extraction melissa defect closed major bio-formats serious fixed
#389 Add support for BD Pathway datasets melissa enhancement closed major bio-formats-4.2 bio-formats non-issue fixed
#390 Bio-Formats Exporter plugin fails with virtual stacks melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#391 Bio-Formats Exporter should use saveBytes instead of saveImage melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#392 Endianness problem when exporting 16-bit ICS melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#393 openThumbImage throws an exception for int16 images melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#394 Flex file metadata objective extraction incorrect melissa defect closed major bio-formats-4.1 bio-formats major fixed
#395 Support for non-numerical patterns in FilePattern melissa enhancement closed minor bio-formats-4.2.1 bio-formats non-issue fixed
#396 Create bfsave.m script for MATLAB melissa enhancement closed minor bio-formats non-issue fixed
#397 Add support for .nex file format melissa task closed major bio-formats-5.0 bio-formats non-issue fixed
#398 Better support for N-dimensional data curtis enhancement closed major bio-formats-5.0 bio-formats serious fixed
#399 Remove deprecated methods from AWTImageTools melissa task closed minor bio-formats-4.2 bio-formats serious fixed
#400 Remove IFormatReader.openImage in favor of BufferedImageReader class melissa task closed major bio-formats-4.2 bio-formats serious fixed
#401 Split TiffTools into multiple utility classes melissa task closed minor bio-formats-4.2 bio-formats non-issue fixed
#402 Split original metadata fields into series-specific tables melissa defect closed major bio-formats-4.1 bio-formats serious fixed
#403 Buttons in importer series dialog are misaligned melissa defect closed major bio-formats-4.1 plugins serious fixed
#404 Exporter plugin doesn't preserve metadata melissa defect closed minor bio-formats-4.1 plugins serious fixed
#405 OME-TIFF export erroneously reuses OME metadata from input dataset melissa defect closed major bio-formats-4.1 plugins critical fixed
#406 Split channels on export if there are 2 or >=4 16-bit RGB channels melissa task closed major bio-formats-4.1 bio-formats major fixed
#407 Add support for Slidebook spool (.spl) files melissa task closed major bio-formats-4.2 bio-formats non-issue fixed
#408 Exception when opening files with > 512 series in ImageJ melissa defect closed major bio-formats-4.1 plugins serious fixed
#409 int8 BufferedImages are displayed incorrectly melissa defect closed major bio-formats-4.1 bio-formats major fixed
#410 showinf's -fast flag adjusts data too naively melissa defect closed minor bio-formats serious fixed
#411 Add support for Olympus ScanR melissa enhancement closed minor bio-formats-4.1 bio-formats non-issue fixed
#412 Add support for scanning microscopy formats melissa enhancement closed minor bio-formats-5.0 bio-formats non-issue fixed
#413 Very large images cannot be saved melissa defect closed major bio-formats-4.2 bio-formats major fixed
#414 Serialize reader state curtis enhancement closed major bio-formats-5.0 bio-formats serious fixed
#415 Lossless JPEG codec performs invalid bit operations melissa defect closed major bio-formats-4.1 bio-formats major fixed
#416 Feedback 17 melissa defect closed critical from QA serious invalid
#417 Feedback 144:showinf fails on remove invocation melissa defect closed critical from QA serious invalid
#418 Feedback 134: multithreading issue melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#419 Feedback 140: NPE in reader melissa defect closed critical from QA serious fixed
#420 Feedback 145: exported tiffs cannot be opened with melissa defect closed critical from QA serious fixed
#421 Feedback 853: flex reader finds other directories melissa defect closed critical from QA serious invalid
#422 Feedback 855: flex reader not finding server melissa defect closed critical from QA serious fixed
#423 Feedback 856: Add "get imported file-endings" method melissa enhancement closed critical bio-formats-5.0 from QA serious fixed
#424 Feedback 862: mias dataset as timeseries?? melissa defect closed critical from QA serious fixed
#425 FB 863: Allow sending feedback from loci tools melissa enhancement closed major bio-formats-5.0 plugins non-issue fixed
#426 Feedback 890: FlexReader.mapServer too unforgiving melissa defect closed critical from QA serious fixed
#427 Add support for Imacon (.fff) files melissa enhancement closed minor bio-formats-4.2 bio-formats non-issue fixed
#428 Add enumeration for OME-XML versions melissa enhancement closed minor bio-formats minor fixed
#429 Feedback 1020 : ArrayIndexOutOfBounds w/ InCell melissa defect closed critical from QA serious fixed
#430 Feedback 1018: ArrayIndexOutOfBounds in ZeissLSM melissa defect closed critical from QA serious fixed
#431 Feedback 1012: ArrayIndexOutOfBound in Slidebook melissa defect closed critical from QA serious fixed
#432 Feedback 1022: bioformats version # is still 4.0.1 melissa defect closed critical from QA serious fixed
#433 Consider adding getBitsPerPixel() to IFormatReader melissa enhancement closed major bio-formats-4.2 bio-formats non-issue fixed
#434 Feedback 1528: OOM in ZVI melissa defect closed critical from QA serious fixed
#435 Feedback 1526: String index error melissa defect closed critical from QA serious fixed
#436 Improve ND2 initialization time melissa defect closed major bio-formats-4.2 bio-formats minor fixed
#437 Feedback 1692: incell reader OOMs on text parse melissa defect closed critical from QA serious fixed
#438 Allow readers to report whether or not companion files can be expected melissa enhancement closed major bio-formats-4.2 bio-formats non-issue fixed
#439 Add support for HDF files produced by Huygens melissa enhancement closed minor bio-formats-5.0 bio-formats non-issue fixed
#440 Add option to disable file grouping melissa enhancement closed major bio-formats-4.2 plugins serious fixed
#441 Feedback 2110 : File handle error on MIAS plate melissa defect closed critical from QA serious invalid
#442 Feedback 2117: color on change on re-import melissa defect closed critical from QA serious invalid
#443 Add support for IN Cell 3000 datasets melissa enhancement closed major bio-formats-4.3 bio-formats serious fixed
#444 Feedback 2163: ArrayIndexOutOfBound on MicroManage melissa defect closed critical from QA serious fixed
#445 Feedback 2160: Leica lambda scans melissa defect closed critical from QA serious fixed
#446 Feedback 2147: ArrayIndexOutOfBounds with ZeissLsm melissa defect closed critical from QA serious duplicate
#447 Feedback 2138: unknown file format "...ome.xml" melissa defect closed critical from QA serious fixed
#448 Feedback 1689 melissa defect closed critical from QA serious fixed
#449 Feedback 152: IOException rather than FormatExcept melissa defect closed critical from QA serious fixed
#450 Feedback 1489: OMX regression? melissa defect closed critical from QA serious invalid
#451 Feedback 1021: ArrayIndexOutOfBounds in IncellRead melissa defect closed critical from QA serious fixed
#452 Feedback 939: eps "max search length" melissa defect closed major bio-formats-4.2 from QA serious fixed
#453 Feedback 879: invalid opcode in PictReader melissa defect closed critical from QA serious fixed
#454 Feedback 860: NumberFormatException for PE melissa defect closed critical from QA serious fixed
#455 Add support for Zip files with multiple entries melissa enhancement closed minor bio-formats-5.0 bio-formats minor fixed
#456 Add support for half-float pixel data in TIFF files melissa enhancement closed minor bio-formats-4.2 bio-formats minor fixed
#457 Add support for Bio-Rad Gel format melissa enhancement closed major bio-formats-4.2 bio-formats non-issue fixed
#458 Bio-Formats Exporter drops metadata for non-imported images melissa defect closed minor bio-formats-4.2 plugins serious fixed
#459 I/O class review melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#460 Add tests for I/O classes melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#461 Review build system for testing components in isolation melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#462 Review logging infrastructure melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#463 Utility class review melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#464 Review runtime dependencies melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#465 Add tests for ImageJ plugin melissa task closed critical bio-formats-4.2 plugins serious fixed
#466 Review TIFF parsing logic melissa task closed critical bio-formats-4.2 bio-formats serious fixed
#467 Support for Group 3 Fax TIFF compression melissa enhancement closed minor bio-formats serious fixed
#468 TIFF pixel data is incorrect for bit depths that are not a multiple of 8 melissa defect closed major bio-formats-4.2 bio-formats major fixed
#469 Problems autoscaling 1-bit data melissa defect closed minor bio-formats-4.2 plugins serious fixed
#470 Problems decoding 1-bit LZW data melissa defect closed minor bio-formats-4.2 bio-formats serious fixed
#471 1-bit TIFF data has incorrect valid bits per pixel melissa defect closed minor bio-formats-4.2 bio-formats serious fixed
#472 Bio-Formats plugin for OpenImageIO curtis task closed trivial bio-formats non-issue fixed
#473 Support for CRi .im3 format melissa task closed major bio-formats-5.0 bio-formats non-issue fixed
#474 Add support for Varian FDF format melissa task closed major bio-formats-5.0 bio-formats non-issue fixed
#475 Add support for Intervision MV format melissa task closed major bio-formats-5.0 bio-formats non-issue fixed
#476 AVI files saved using one writer per plane are broken melissa defect closed major bio-formats-4.2 bio-formats major fixed
#477 Add support for Mirax data melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#478 Add support for Hamamatsu NanoZoomer data melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#479 Add support for Trestle slide data melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#480 Add support for Hamamatsu VMS data melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#481 scan-deps.pl does not detect that unit tests depend upon log4j JARs melissa defect closed trivial bio-formats-4.2 build minor fixed
#482 Expand LOCI Hudson job melissa task closed trivial bio-formats-4.2.1 build non-issue fixed
#483 Add support for Matlab matrix files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#484 Investigate usage of FileChannel.map(...) melissa task closed major bio-formats-4.2 bio-formats serious fixed
#485 Support for writing multi-file OME-TIFF datasets melissa defect closed major bio-formats-4.2 bio-formats serious fixed
#486 Generalize support for writing multiple files melissa enhancement closed major bio-formats-4.2 bio-formats serious fixed
#487 Add support for ECAT7 files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#488 Add support for OpenEXR files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#489 Andor TIFF timestamps are missing or incorrect melissa defect closed major bio-formats-4.2 bio-formats serious fixed
#490 Add support for PDS files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#491 Check that Leica LIF physical dimensions are correct melissa defect closed major bio-formats-4.2 bio-formats serious fixed
#492 OME-TIFF reader does not support qualified namespaces melissa defect closed critical bio-formats-4.2 bio-formats critical fixed
#493 Series beyond 456 do not appear in ImageJ plugin curtis defect closed critical bio-formats-4.2 plugins serious fixed
#494 ImageJ importer plugin does not preserve pixel sizes curtis defect closed major bio-formats-4.2 plugins major fixed
#495 Lookup tables are not correctly applied if there is one LUT per channel curtis defect closed major bio-formats-4.2 plugins serious fixed
#496 Leica lookup tables not applied when metadata collection disabled melissa defect closed minor bio-formats-4.2 bio-formats serious fixed
#497 Allow user to specify dimensions during stack concatenation melissa enhancement closed major bio-formats-5.0 plugins minor fixed
#498 Consider using either JUnit or TestNG for all tests melissa task closed minor bio-formats-5.0 test-suite non-issue fixed
#499 AVI writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#500 APNG writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#501 Java writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#502 JPEG-2000 writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#503 JPEG writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#504 OME-XML writer does not support saving tiles melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#505 TIFF writer does not support saving tiles whose width is smaller than the full image width melissa defect closed critical bio-formats-5.0 bio-formats serious fixed
#506 Color mode settings do not work for single-channel images curtis defect closed major bio-formats-4.2.1 plugins serious fixed
#507 Exception importing 16-bit indexed color data curtis defect closed major bio-formats-4.2.1 plugins serious fixed
#508 Allow unit tests to be randomized melissa task closed minor bio-formats-4.3 test-suite non-issue fixed
#509 Add test for macro key regressions melissa task closed minor bio-formats-5.0 test-suite non-issue fixed
#510 Some Amira files throw an exception during setId melissa defect closed major bio-formats-4.2.1 bio-formats minor invalid
#511 Compressed Amira file not read properly melissa defect closed major bio-formats-4.2.1 bio-formats minor fixed
#512 Logging cleanup melissa task closed minor bio-formats-4.2 bio-formats cosmetic fixed
#513 Exporting RGB images to OME-TIFF fails melissa defect closed critical bio-formats-4.2.1 bio-formats major fixed
#514 Fix Image5D and View5D view modes curtis defect closed minor bio-formats-4.2.1 plugins serious fixed
#515 Investigate physical size population for ScanR datasets melissa task closed minor bio-formats-4.2.1 bio-formats serious fixed
#516 Allow metadata support documentation to be fully autogenerated melissa enhancement closed minor bio-formats-4.2.1 docs non-issue fixed
#517 Bio-Formats Importer progress bar is missing on some systems melissa defect closed major bio-formats-4.2.1 plugins serious worksforme
#518 Allow exporter plugin to export to multiple files melissa enhancement closed minor bio-formats-5.0 plugins non-issue fixed
#519 Implement new saveImage methods in BufferedImageWriter melissa task closed minor bio-formats-4.2.1 bio-formats minor fixed
#520 Verify that generated OME-XML validates melissa task closed major bio-formats-4.2.1 bio-formats serious fixed
#521 Make Ant fail when tests fail melissa task closed major bio-formats-4.2.1 test-suite non-issue fixed
#522 Add support for Fuji LAS 3000 files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#523 Bio-Formats Windowless Importer is broken melissa defect closed major bio-formats-4.2.1 bio-formats major fixed
#524 Better documentation for command line tools melissa task closed major bio-formats-4.2.1 bio-formats major fixed
#525 Files cannot be saved from ImageViewer unless '-omexml' option was passed to showinf melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#526 Parse metadata from S-FEG and Helios NanoLab TIFF files melissa enhancement closed major bio-formats-4.2.1 bio-formats serious fixed
#527 Add support for multiple positions in one Zeiss LSM file melissa defect closed major bio-formats-4.2.1 bio-formats minor fixed
#528 LUTs are lost in virtual stack mode melissa defect closed minor bio-formats-4.2.1 plugins serious fixed
#529 Parse metadata from TIFFs produced by Nikon Elements melissa enhancement closed major bio-formats-4.2.1 bio-formats minor fixed
#530 BD Pathway reader doesn't fully populate original metadata hashtable melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#531 Add md5 test for sub-images melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#532 Add test for leaking file handles melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#533 Add test that reads planes in a random order melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#534 Add test for consistent type checking melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#535 Allow tests to be run on files in memory melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#536 Consider changing test configuration file format melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#537 Add tests for non-core metadata consistency melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#538 Allow MD5 tests to accept an alternate hash melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#539 Skip tests when setId fails melissa enhancement closed minor bio-formats-5.0 test-suite non-issue fixed
#540 Add Hudson jobs to run data-driven tests melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#541 Add support for Varian FID files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#542 Multi-series stitching is incorrect melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#543 OMETiffWriter.close() can leak file descriptors melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#544 Native support for Quicktime Sorenson 1 codec (SVQ1) melissa enhancement closed trivial bio-formats minor fixed
#545 Fix TIFF/OME-TIFF export with JPEG/JPEG-2000 compression melissa defect closed critical bio-formats-4.2.1 bio-formats serious fixed
#546 Make findbugs happy melissa task closed major bio-formats-5.0 bio-formats minor fixed
#547 Add system property values to ImageJ plugins log melissa enhancement closed major bio-formats-4.2.1 plugins non-issue fixed
#548 Support OME-XML with BinData.Length = 0 callan defect closed major bio-formats serious fixed
#549 Some options should be disabled in the "Standard ImageJ" view mode melissa defect closed major bio-formats-4.2.1 plugins serious fixed
#550 ScanR reader assumes that wells form a square melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#551 "waitTime" not parsed from Prairie datasets melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#552 Add support for Zeiss .lms files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#553 Add support for Zeiss Axiovision TIFFs melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#554 Exporting a multi-series OME-TIFF file results in incorrect pixel data melissa defect closed major bio-formats-4.2.1 bio-formats critical fixed
#555 OME-TIFF reader resets Image Name melissa defect closed minor bio-formats-4.2.1 bio-formats serious fixed
#556 OME-TIFF reader should use MetadataOnly rather than BinData melissa defect closed minor bio-formats-4.2.1 bio-formats serious fixed
#557 Virtual stack channel-specific LUTs are not preserved melissa defect closed major bio-formats-4.2.1 plugins serious fixed
#558 MetaMorph ND handling for underscores callan defect closed major bio-formats-4.2.1 bio-formats major fixed
#559 LSM reader XT linescan opened as XY melissa defect closed minor bio-formats-5.0 bio-formats serious fixed
#560 Fix multi-line description MetaMorph ND files callan defect closed minor bio-formats minor fixed
#561 ServiceFactory file handle leak melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#562 MIAS import fails with NPE melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#563 Add support for OME-TIFF files produced by Leica Matrix scanner melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#564 Improve original metadata population in OME-XML melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#565 Expand (and clean up) use of new 'setWriteSequentially' method melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#566 Fix tests in ome-xml component melissa defect closed major bio-formats-4.2.1 test-suite major fixed
#567 LUTs not parsed from .pcx files melissa defect closed minor bio-formats-4.2.1 bio-formats minor fixed
#568 Review results of testing project melissa task closed minor bio-formats-4.3 bio-formats non-issue fixed
#569 Add support for JPEG-compressed AVIs melissa enhancement closed minor bio-formats-5.0 bio-formats minor fixed
#570 Populate ImageJ's 'origin' metadata melissa enhancement closed major bio-formats-4.2.1 plugins cosmetic fixed
#571 Bug when Pump is used in a LightSourceSettings callan defect closed blocker bio-formats-4.2.1 bio-formats serious fixed
#572 Location tests can fail when /tmp is under high load melissa defect closed minor bio-formats-4.2.1 bio-formats minor fixed
#573 Add support for Olympus CellSens .vsi data melissa enhancement closed major bio-formats-4.3 bio-formats non-issue fixed
#574 Some Prairie datasets take a long time to initialize on Windows melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#575 Make it easier to get/set the pixels' compression type melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#576 Improve Zeiss LSM stage/tile position parsing melissa enhancement closed major bio-formats-4.2.1 bio-formats serious fixed
#577 Switch Leica LIF reader to use DOM parsing (instead of SAX) melissa task closed major bio-formats-4.3 bio-formats minor fixed
#578 bfconvert does not properly overwrite or append to files melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#579 Images do not properly update in the Data Browser melissa defect closed critical bio-formats-4.2.1 plugins major fixed
#580 Virtual stack with split channels, timepoints and/or planes melissa enhancement closed major bio-formats-4.3 plugins non-issue fixed
#581 Add support for DICOM supplement #145 melissa enhancement closed major bio-formats-4.3 bio-formats non-issue fixed
#582 Consider standarizing some original metadata keys melissa task closed minor bio-formats-5.0 bio-formats non-issue fixed
#583 DeltaVision OMX read error melissa defect closed major bio-formats-4.2.1 bio-formats serious fixed
#584 Data repository cleanup melissa task closed critical bio-formats-4.3 test-suite critical fixed
#585 Make error message windows more friendly melissa enhancement closed major bio-formats-5.0 plugins cosmetic fixed
#586 Preserve custom color options melissa defect closed major bio-formats-4.3 plugins minor fixed
#587 Move color options to a separate dialog melissa enhancement closed major bio-formats-5.0 plugins cosmetic fixed
#588 Consider writing decoder for compressed Flex files melissa enhancement closed major bio-formats non-issue fixed
#589 Add support for TIFF files with FillOrder == 2 melissa enhancement closed major bio-formats-5.0 bio-formats minor fixed
#590 Series dialog should indicate the total number of series melissa enhancement closed major bio-formats-5.0 plugins cosmetic fixed
#591 Writers do not support overwriting metadata melissa enhancement closed major bio-formats-5.0 bio-formats serious fixed
#592 Slidebook pixel data is not always correct melissa defect closed critical bio-formats-4.3 bio-formats serious fixed
#593 Add support for Micro-CT VOL files melissa enhancement closed major bio-formats-5.0 bio-formats non-issue fixed
#594 Double-check Image -> ROI linkages melissa task closed major bio-formats-5.0 bio-formats minor fixed
#595 Overwriting compressed planes doesn't always work melissa defect closed major bio-formats-5.0 bio-formats serious fixed
#596 Recorded macros contain "open" twice melissa defect closed major bio-formats-4.3 plugins minor fixed
#597 Add support for .aim files melissa enhancement closed major bio-formats-4.3 bio-formats non-issue fixed
#598 ImageViewer's file chooser extensions are wrong melissa defect closed minor bio-formats-5.0 bio-formats minor fixed
#599 Add optimal tile size methods melissa task closed critical bio-formats-4.3 bio-formats non-issue fixed
#600 Make sure that JPEG-2000 decoding works in parallel melissa task closed critical bio-formats-4.3 bio-formats minor fixed
#601 Investigate using MediaUtil for block-based JPEG decoding melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#602 Move MetadataLevel, MetadataOptions, and DefaultMetadataOptions melissa task closed major bio-formats-4.3 bio-formats non-issue fixed
#603 Move get/setMetadataOptions methods to IFormatReader melissa task closed major bio-formats-4.3 bio-formats non-issue invalid
#604 Move "no OME-XML" message out of OMETiffReader melissa task closed minor bio-formats-4.3 bio-formats cosmetic fixed
#605 OMEXMLMetadata objects used by OMETiffWriter can not be re-used melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#606 Try to eliminate the updater's file renaming requirement on Windows melissa task closed minor plugins minor fixed
#607 Drag and drop on shortcut window produces "Open" dialog melissa defect closed major bio-formats-4.3 plugins serious fixed
#608 Zip file URLs are not supported melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#609 Add option to bfconvert for saving autoscaled images melissa enhancement closed minor bio-formats cosmetic fixed
#610 Some AVI files have skewed scanlines melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#611 ICS export should preserve more metadata melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#612 Multi-channel indexed color images treated incorrectly melissa defect closed major bio-formats-4.3 plugins serious fixed
#613 Investigate consolidating 'showinf' and 'bfview' melissa task closed minor bio-formats-4.3 bio-formats cosmetic fixed
#614 Write documentation on which files can be picked in each format melissa task closed minor bio-formats-5.0 docs non-issue fixed
#615 Add special case to Openlab LIFF plane name parsing melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#616 Openlab LIFF reader assumes non-sparse planes melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#617 Channel order is reversed in some LSM files melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#618 Certain JPEG-2000 files are not read correctly melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#619 Add tests for ScreenReader melissa task closed major bio-formats-4.3 bio-formats serious fixed
#620 OpenlabReader thread safety callan defect closed major bio-formats-4.3 bio-formats serious fixed
#621 Some ND2 files are not read completely melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#622 .aim to TIFF conversion is not quite right melissa defect closed major bio-formats-4.3 bio-formats serious invalid
#623 Expand InCell support to cover InCell 2000 callan enhancement closed major bio-formats-4.3 bio-formats minor fixed
#624 Allow FileStitcher to stitch files with multiple series melissa enhancement closed major bio-formats-4.3 bio-formats serious fixed
#625 Add support for MetaXpress data melissa enhancement closed major bio-formats non-issue fixed
#626 Slidebook valid bits per pixel not parsed melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#627 Slidebook series grouping is not always correct melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#628 Update ScreenReader to handle InCell 3000 data melissa enhancement closed major bio-formats-4.3 bio-formats minor fixed
#629 Add support for Leica Stereo Microscope data melissa task closed major bio-formats non-issue fixed
#630 Bio-Rad LUTs do not look correct melissa defect closed minor bio-formats-4.3 bio-formats cosmetic fixed
#631 EPS coloring is often incorrect melissa defect closed minor bio-formats-4.3 bio-formats minor fixed
#632 Some metadata is not populated for Zeiss LSM files melissa defect closed minor bio-formats-4.3 bio-formats minor fixed
#633 FV1000 LUTs are not displayed correctly in ImageJ melissa defect closed minor bio-formats-4.3 plugins minor fixed
#634 File grouping does not work in ImageJ on Windows melissa defect closed major bio-formats-4.3 plugins serious fixed
#635 Add support for Image-Pro .ips metadata files melissa enhancement closed major bio-formats non-issue fixed
#636 Allow ImageReader to call isThisType(..., false) melissa task closed minor bio-formats-4.3 bio-formats minor fixed
#637 Plane numbers in status bar are sometimes incorrect melissa defect closed minor bio-formats-4.3 plugins cosmetic fixed
#638 Add support for Zeiss LSM files that have differing bits per sample melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#639 Make sure that static fields are being used properly melissa task closed major bio-formats-4.3 bio-formats minor fixed
#640 Add a few more options to bfconvert melissa enhancement closed major bio-formats non-issue fixed
#641 Add support for Zeiss FCS files melissa enhancement closed major bio-formats non-issue fixed
#642 Add better isThisType tests melissa enhancement closed minor bio-formats-4.3 test-suite non-issue fixed
#643 Slidebook files with maximum projections cannot be read melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#644 Parse additional Andor TIFF tags melissa enhancement closed major bio-formats-4.3 bio-formats minor fixed
#645 Eliminate log4j warning messages melissa defect closed major bio-formats-4.3 bio-formats cosmetic fixed
#646 OME-TIFFs cannot be opened in Fiji with file grouping turned on melissa defect closed major bio-formats-4.3 bio-formats serious fixed
#647 Add conversion convenience methods to FormatTools melissa enhancement closed major bio-formats non-issue fixed
#648 Add reader wrapper that provides simpler tile access melissa enhancement closed major bio-formats non-issue fixed
#649 Add IFormatWriter.saveBytes signatures that accept a Region melissa enhancement closed major bio-formats non-issue fixed
#650 Update tiffcomment to allow editing on the command line melissa enhancement closed minor bio-formats-4.3 bio-formats minor fixed
#651 Allow JPEG-2000 writer to use lossy compression melissa enhancement closed major bio-formats-4.3 bio-formats minor fixed
#652 Create a web site for slim-curve aivar task closed minor slimplugin1.2 slim-curve non-issue fixed
#653 Add support for non-exp fns to curve fitter class aivar enhancement closed major slim-curve non-issue fixed
#654 Basic UI and graphical output aivar task closed major slimplugin2.0 slim-curve non-issue fixed
#655 Import ecf global curve library aivar task closed major slim-curve non-issue fixed
#656 Check what is meant by an 'iteration' and provide for this in ecf class. aivar task closed major slimplugin2.0 slim-curve non-issue fixed
#657 Add fit execution framework aivar feature closed major slimplugin2.0 slim-curve non-issue fixed
#658 Global fitting causes problem with Gauss Jordan when B is NULL. aivar defect closed major slim-curve serious fixed
#659 Error field is not filled correctly on time resolved front panel aivar defect closed major slimplugin2.0 slim-curve serious fixed
#660 Non-instr versions of the functions not implemented aivar defect closed major slim-curve serious fixed
#661 Post-acquisition Forward workflow amjohnson27 task closed minor forward non-issue moved
#662 Controlled vocabulary for Forward subject terms amjohnson27 task closed minor forward non-issue moved
#663 Direct links to OME-TIFF datasets amjohnson27 task closed minor forward non-issue moved
#664 SLIM Plugin: Fitting engine rework aivar feature closed major slimplugin1.1 slim-plugin serious fixed
#665 Provide Histogram tool for SLIM Plugin aivar defect closed major slim-plugin serious fixed
#666 SLIM Curve: Fix GCI_marquardt_estimate_errors aivar defect closed major slimplugin2.0 slim-curve serious fixed
#667 Create multi-platform version of SLIM Plugin aivar task closed minor slimplugin2.0 slim-plugin minor fixed
#668 Package SLIM Plugin release aivar defect closed major slimplugin1.0 slim-plugin serious duplicate
#669 SLIM Curve/SLIM Plugin: Add additional TRI2 fitting capabilities aivar defect closed major slimplugin2.0 slim-curve minor fixed
#670 SLIM Plugin: Clean up UI aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#671 SLIM Plugin: fix display plugin concept aivar feature closed minor slimplugin2.0 slim-plugin serious fixed
#672 SLIM Curve/SLIM Plugin add parameter constraints aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#673 Remove transitive dependencies from the cppwrap-maven-plugin POM curtis task closed minor build minor fixed
#674 SLIMPlugin: Ensure TRI2 and SLIMPlugin results agree aivar feature closed critical slimplugin1.1 slim-plugin serious fixed
#675 SLIM Plugin: Handle odd photon counts aivar defect closed minor slimplugin1.0 slim-plugin minor fixed
#676 SLIM Plugin: automatic refit broken aivar defect closed minor slimplugin1.0 slim-plugin minor fixed
#677 SLIM Plugin: Initial fit aivar enhancement closed minor slimplugin1.0 slim-plugin minor fixed
#678 Transient cursors not applied properly aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#679 Fitted transient graph problems aivar defect closed minor slimplugin1.0 slim-plugin minor fixed
#680 Cursors are flakey aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#681 Plugin fails if lifetime LUT missing. aivar defect closed major slimplugin1.0 slim-plugin minor fixed
#682 SLIM Plugin: Flakey fitting aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#683 SLIM Plugin: Plugin confused whether there is a prompt. aivar defect closed major slimplugin1.1 slim-plugin major fixed
#684 average IRF aivar enhancement closed minor slimplugin2.0 slim-plugin minor fixed
#685 phasor plot aivar enhancement closed trivial slimplugin2.0 slim-plugin non-issue fixed
#686 Log / Linear Scale on Fit y-axis aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#687 Display number of photons in fit aivar enhancement closed major slimplugin1.1 slim-plugin serious fixed
#688 Creating fractional intensity and fractional contribution images from A images aivar enhancement closed major slim-plugin serious fixed
#689 Ability to Mask from histogram - change non-included pixels to 0 aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#690 Multi-layered filtering aivar enhancement closed minor slimplugin2.0 slim-plugin minor fixed
#691 Saving Cursors with each tif image aivar enhancement closed minor slimplugin2.0 slim-plugin minor fixed
#692 Save instrument responses (IRF) as ics instead of .irf aivar enhancement closed minor slimplugin2.0 slim-plugin minor fixed
#693 Fitted plot lacking on decay graph sometimes aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#694 Fitted results off aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#695 SLIMPlugin: Problem finding LUT when running from a shortcut. aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#696 Fitted results off, no fitted line shown aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#697 Sometimes TRI2 and SLIMPlugin results agree, except for chi-square aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#698 TRI2 and SLIM Plugin prompt cursors differ aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#699 Closing Histogram Tool makes it go away for the session aivar defect closed minor slimplugin1.2 slim-plugin minor fixed
#700 Binning is broken aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#701 Lifetime LUT has too much green aivar defect closed minor slimplugin2.0 slim-plugin minor fixed
#702 Optional colorized grayscale fitted images aivar enhancement closed major slimplugin1.1 slim-plugin major fixed
#703 Iniital decay chart lacking vertical cursors aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#704 Histogram Tool min/max not always updated aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#705 Truncate floating point results aivar defect closed minor slimplugin2.0 slim-plugin minor fixed
#706 Entering new prompt cursor values doesn't update prompt graph cursors aivar defect closed major slimplugin1.1 build serious fixed
#707 Unable to change excitation delay in UI panel aivar defect closed major slimplugin1.0 slim-plugin serious fixed
#708 Add option to specify additional library and/or include paths curtis enhancement closed minor jar2lib serious moved
#709 Create jar2ice and icewrap Maven plugin curtis task closed minor jar2lib non-issue wontfix
#710 Add ability to limit which proxies are generated curtis enhancement closed major jar2lib serious moved
#711 Bi-exponential fit results don't agree with TRI2 aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#712 Tri-exponential fit results don't agree with TRI2 aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#713 Stretched exponential fit results don't agree with TRI2 aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#714 Stretched exponential graph is wrong aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#715 Single exponential results disagree aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#716 Fitting with a prompt gives bad results. aivar defect closed major slimplugin1.1 slim-plugin major fixed
#717 Can't fix parameters aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#718 Problems with some SDT files aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#719 Get NetID authentication working for Microscopy web site curtis enhancement closed minor other non-issue moved
#720 Problems with gpl1.sdt aivar defect closed major slimplugin1.1 slim-plugin serious fixed
#721 Inconsistencies when masking fitted images aivar defect closed minor slimplugin2.0 slim-plugin serious fixed
#722 Histogram tool needs to automatically zoom in aivar defect closed major slimplugin2.0 slim-plugin major fixed
#723 Can't open two lifetime images at once aivar defect closed major slimplugin2.0 slim-plugin major fixed
#724 Show tau mean fitted images aivar defect closed major slimplugin1.1 slim-plugin minor fixed
#725 Add higher amounts of binning aivar defect closed major slimplugin2.0 slim-plugin minor fixed
#726 Save histogram data aivar defect closed major slimplugin2.0 slim-plugin minor fixed
#727 SLIM Plugin Milestone 1.1 : Beta for ImageJ 1 aivar task closed major slimplugin1.1 slim-plugin serious fixed
#728 SLIM Plugin Milestone 1.2 : Release in ImageJ 2 aivar task closed major slimplugin2.0 slim-plugin serious fixed
#729 Gray scale image should be part of masking scheme aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#730 Automatic refit is flakey aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#731 Remove unimplemented features from UI aivar task closed minor slimplugin1.2 slim-plugin serious fixed
#732 Mirror new TRI2 rounding scheme aivar task closed major slimplugin1.2 slim-plugin serious fixed
#733 Automatic refit for summed image aivar defect closed minor slimplugin1.2 slim-plugin serious fixed
#734 Show 3D lifetime histogram with chisquare dimension aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#735 Masked pixels should appear with NaN value aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#736 Fitted images can have improper min/max ranges aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#737 Sum all pixels ignores hidden pixels aivar defect closed minor slimplugin2.0 slim-plugin minor fixed
#738 Unchecking "Hide all Pixels" leaves Histogram Tool cursors in wrong positions aivar defect closed major slimplugin2.0 slim-plugin cosmetic fixed
#739 Summed fitted results are bad sometimes aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#740 Estimate Cursors w/o Prompt is bad aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#741 SLIMPlugin threshold control doesn't correspond to TRI2 aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#742 UI panel text fields fail to trigger refit aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#743 TRI2/SP fitted parameter initial guess issues aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#744 SP fitted images don't handle errors aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#745 Show AIC as well as chi-square aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#746 Batch processing aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#747 Excitation window should have log checkbox aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#748 Histogram zoom when hiding pixels is flaky aivar defect closed minor slimplugin1.2 slim-plugin serious fixed
#749 Autoranging min/max on histogram tool doesn't account for hidden pixels aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#750 Histogram tool needs a way to measure Gaussian distribution centers aivar defect closed minor slimplugin2.0 slim-plugin serious fixed
#751 Need to distinguish sets of fitted images. aivar defect closed minor slimplugin1.2 slim-plugin serious fixed
#752 Should show crosshair for fitted pixel aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#753 Threshold mask doesn't work when binning is in effect. aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#754 Remove initial logging message aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#755 Verify bf-itk-pipe plugin can fully read/write images that don't fit in memory hinerm defect closed major other major worksforme
#756 Fitting a single photon count crashes aivar defect closed major slimplugin2.0 other serious invalid
#757 Add decay image file name to fitted images aivar enhancement closed trivial slimplugin1.2 slim-plugin minor fixed
#758 Honor ROIs when fitting images aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#759 Histogram should autoscale to hide rogue high values aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#760 Information about the fit should be saved along with fitted images aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#761 Hidden pixels get out of synch aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#762 BF-ITK doesn't write multi-channel images properly hinerm defect closed major other serious fixed
#763 BF-ITK doesn't preserve LUTs hinerm defect closed major other serious fixed
#764 Histogram tool should have logarithmic checkbox aivar defect closed minor slimplugin1.2 slim-plugin serious fixed
#765 fix export txt aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#766 green pixel update aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#767 add percent A1 and A2 columns aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#768 histogram export aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#769 BATCH!!! PLEASE PLEASE PLEASE aivar defect closed major slimplugin2.0 slim-plugin serious duplicate
#770 Prairie reader is very slow in populating metadata curtis enhancement closed major bio-formats serious moved
#771 Use 0% by default when stitching from metadata curtis enhancement closed major fiji serious moved
#772 Disentangle stage positions from time points curtis defect closed major bio-formats serious fixed
#773 Support for truncated Prairie datasets curtis enhancement closed major bio-formats serious fixed
#774 Problems fitting multiple channels aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#775 Fitting multiple channels skips pixels aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#776 Fitting channels sometimes displays wrong image aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#777 Fitting channels, threshold, error & hidden pixels not displayed correctly on grayscale image aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#778 Fitting channel stack, slider won't update histogram aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#779 Batch mode improvements aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#780 Batch mode, save & restore user settings aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#781 Batch mode, automatically threshold each image aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#782 Batch mode, allow saving pixels & histograms to separate files aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#783 Batch mode, combine images for histogram aivar defect closed major slimplugin1.2 other serious fixed
#784 Problematic FLIM file aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#785 Can't open two images serially aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#786 Default histogram s/b non-logarithmic aivar defect closed trivial slimplugin1.2 slim-plugin serious fixed
#787 Compare SLIM Plugin and SPC Image results aivar defect closed major slimplugin1.2 slim-plugin major fixed
#788 SLIM Plugin grayscale overflow issue aivar defect closed minor slimplugin1.2 slim-plugin serious fixed
#789 Fitted decay graph doesn't scale well aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#790 Exported histograms should report A as a %, not raw aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#791 Numeric fields in UI need a spinner aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#792 Better UI for selecting which fitted images to produce aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#793 Export histograms in table form aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#794 Resize histogram taller aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#795 Resize grayscale image larger aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#796 Resize decay graph larger aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#797 Show chi-square on decay graph aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#798 Show IRF on decay graph aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#799 Evaluate need for fitted scatter parameter aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#800 Add histogram smoothing aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#801 Misinterpretation of Double.MIN_VALUE aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#802 Residuals should be weighted aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#803 Save/restore settings aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#804 Batch mode needs progress bar aivar defect closed major slimplugin1.2 slim-plugin minor fixed
#805 window resizing screws up histogram aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#806 .csv aivar enhancement closed major slimplugin2.0 slim-plugin serious fixed
#807 batch histogram display aivar enhancement closed major slim-plugin serious fixed
#808 summary aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#809 Batch mode summary histogram numbers off aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#810 Batch mode summary histogram support non-T parameters aivar defect closed major slimplugin1.2 slim-plugin serious fixed
#811 irf bugs aivar defect closed critical slimplugin1.2 slim-plugin critical fixed
#812 prompt aivar enhancement closed major slim-plugin serious fixed
#813 hide pixels outside of range aivar defect closed major slim-plugin serious worksforme
#814 won't open or create IRF aivar defect closed major slim-plugin serious fixed
#815 why is my slim plugin broken. aivar defect closed major slim-plugin serious fixed
#816 Indicate batch mode available aivar defect closed major slim-plugin serious fixed
#817 Support SDT and ICS files aivar defect closed major slim-plugin serious fixed
#818 Support median filtering of colorized fitted images aivar defect closed major slim-plugin serious fixed
#819 Support ROIs aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#820 Display montage of fitted images in a single window aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#821 Allow scripting SLIM Plugin aivar defect closed major slimplugin2.0 slim-plugin serious fixed
#822 Improve SLIM Curve test program aivar enhancement closed minor slim-curve serious fixed