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Ticket #772 (closed defect: fixed)

Opened 2012-11-26T14:17:45-06:00

Last modified 2013-01-31T14:58:16-06:00

Disentangle stage positions from time points

Reported by: curtis Owned by: curtis
Priority: major Milestone:
Component: bio-formats Severity: serious
Keywords: prairie Cc: kmriching, ponik@…
Blocked By: Blocking:


Kristin Riching writes:

I have a dataset that I collected on the Prairie Confocal that contains 5 different x-y fields each containing a z-stack and time series. I would like to be able to open 5 hyperstacks in Fiji that correspond to each field, but I'm not sure if Bioformats currently supports this, unless I am not checking the appropriate checkboxes. Right now I am getting one hyperstack that cycles through each x-y field at every time point.

The issue is that AFAICT, the Prairie file format makes no distinction between stage positions and time points, referring to both as "Sequences." To differentiate them, we must study the stage position coordinates themselves and infer the relationship.

Change History

comment:1 Changed 2012-11-26T14:21:17-06:00 by curtis

Work was begun on this feature on the  prairie-fixes branch ( PR #217). The disentanglement logic is in place, which divides the dataset properly, but the actual reader does not yet respect that division.

comment:2 Changed 2012-11-29T15:16:34-06:00 by curtis

  • Cc ponik@… added

comment:3 Changed 2012-12-07T15:58:25-06:00 by curtis

  • Keywords prairie added

comment:4 Changed 2013-01-11T16:21:19-06:00 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:5 Changed 2013-01-31T14:58:16-06:00 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.