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Ticket #622 (closed defect: invalid)

Opened 2010-12-11T12:18:23-06:00

Last modified 2010-12-22T12:45:56-06:00

.aim to TIFF conversion is not quite right

Reported by: melissa Owned by: melissa
Priority: major Milestone: bio-formats-4.3
Component: bio-formats Severity: serious
Keywords: Cc: harryh@…
Blocked By: Blocking:

Description

Specifically: 

> 1. The depth of 30205 microns in the original AIM file seems to have been replaced by 863cm, which looks like a 1cm/plane conversion.
> 
> 2. The voxel size has gone from 35 micron^3 to 0.00x0.00x1cm - rounding error, or something else?
> 
> 3 The display range has been changed, going from -7805 - 32767 in the original to  -2220  - 19609 in the tif.

Change History

comment:1 Changed 2010-12-22T12:45:56-06:00 by melissa

  • Status changed from new to closed
  • Resolution set to invalid

This is actually a set of problems in ImageJ's native TIFF reader. I can duplicate all three problems by doing the following:

  • 'bfconvert /path/to/file.aim test.tiff'
  • start Fiji
  • select "File > Open"
  • select test.tiff
  • press 'i'

The displayed info is: 

Title: test.tiff
Width:  1.75 cm (501)
Height:  2.03 cm (581)
Depth:  547.00 cm (547)
Resolution:  285.71 pixels per cm
Voxel size: 0.00x0.00x1 cm
ID: -4
Coordinate origin:  0,0,0
Bits per pixel: 16 (signed)
Display range: -2998 - 24413
Image: 1/547
No Threshold
 
Calibration Function: y = a+bx
  a: -32768.000000
  b: 1.000000
  Unit: "Gray Value"
Path: /home/melissa/test.tiff
 
No Selection

However, if I instead open test.tiff using "Plugins > LOCI > Bio-Formats Importer", then I see the following info: 

 BitsPerPixel = 16
 DimensionOrder = XYCZT
 IsInterleaved = false
 IsRGB = false
 LittleEndian = true
 PixelType = int16
 SizeC = 1
 SizeT = 547
 SizeX = 501
 SizeY = 581
 SizeZ = 1
BitsPerSample = 16
Compression = Uncompressed
ImageLength = 581
ImageWidth = 501
Location = /home/melissa/test.tiff
MetaDataPhotometricInterpretation = Monochrome
MetaMorph = no
NumberOfChannels = 1
PhotometricInterpretation = BlackIsZero
PlanarConfiguration = Planar
ResolutionUnit = Centimeter
SampleFormat = two's complement signed integer
SamplesPerPixel = 1
Software = LOCI Bio-Formats
XResolution = 285
YResolution = 285

------------------------

Title: test.tiff
Width:  17535.02 microns (501)
Height:  20335.02 microns (581)
Resolution:  0.0286 pixels per micron
Voxel size: 35.00x35.00x0 micron
ID: -2
Coordinate origin:  0,0,0
Bits per pixel: 16 (signed)
Display range: -7142 - 32767
Image: 1/547 (t:1/547 - /home/melissa/test.tiff)
No Threshold
 
Calibration Function: y = a+bx
  a: -32768.000000
  b: 1.000000
  Unit: "gray value"
Path: /home/melissa/test.tiff
 
No Selection

The only real difference between that and the original file's info is the physical depth. TIFFs cannot store the physical depth, though, so this is expected. To preserve the physical depth, you would need to convert to OME-TIFF.