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Ticket #773 (closed enhancement: fixed)

Opened 2012-11-26T14:26:08-06:00

Last modified 2013-01-31T14:58:28-06:00

Support for truncated Prairie datasets

Reported by: curtis Owned by: curtis
Priority: major Milestone:
Component: bio-formats Severity: serious
Keywords: prairie Cc: jalast
Blocked By: Blocking:


It is possible to stop an acquisition early in PrairieView, which results in missing TIFF files and XML metadata blocks, and therefore missing planes. Bio-Formats does not handle this situation gracefully, assuming all files and XML are present, and throws an exception if not.

Julie Last writes:

The way [Bill] runs his experiments is that he sets a long time series and then aborts the series after the even he is looking for is finished. Doing this means that the data could end at any focal plane (and not just cut off the last plane).

Change History

comment:1 Changed 2012-11-26T14:27:23-06:00 by curtis

Work was begun on this feature on the  prairie-fixes branch ( PR #217). The initial logic is in place, but the current fix only works when the last focal plane of the series is missing. It does not work properly when additional planes are missing, so further investigation is required.

comment:2 Changed 2012-12-07T15:58:20-06:00 by curtis

  • Keywords prairie added

comment:3 Changed 2013-01-11T16:21:33-06:00 by curtis

This bug is now fixed in the prairie-fixes branch. But since the changes are expansive, we are still verifying that all of our Prairie test data works as expected. Once we are sure everything still works, we will update Fiji and close this ticket.

comment:4 Changed 2013-01-31T14:58:28-06:00 by curtis

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

Fiji has been updated to include the shiny new Prairie support! Run Help > Update Fiji to get the fix.