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Ticket #116 (closed task: fixed)

Opened 2010-06-28T16:12:17-05:00

Last modified 2011-01-14T15:14:21-06:00

Document Bio-Formats usage with FARSIGHT

Reported by: curtis Owned by: hinerm
Priority: critical Milestone: biweekly-2010: Dec-13 to Dec-23
Component: FARSIGHT Version:
Severity: non-issue Keywords:
Cc: Blocked By:
Blocking:

Description

We have instructions for compiling Bio-Formats for use with ITK, but we would also like to document more specifically which FARSIGHT modules can make use of Bio-Formats, and current limitations (unsupported image types, architectures, etc.), including screenshots.

Change History

comment:1 Changed 2010-06-28T16:14:35-05:00 by curtis

  • Status changed from new to accepted

comment:2 Changed 2010-07-12T15:41:21-05:00 by curtis

  • Milestone changed from biweekly-2010: Jun-28 to Jul-09 to biweekly-2010: Jul-12 to Jul-23

comment:3 Changed 2010-07-20T15:00:14-05:00 by curtis

  • Priority changed from major to critical

comment:4 Changed 2010-07-26T10:30:45-05:00 by curtis

  • Milestone changed from biweekly-2010: Jul-12 to Jul-23 to biweekly-2010: Jul-26 to Aug-06

comment:5 Changed 2010-08-16T11:28:06-05:00 by curtis

  • Milestone changed from biweekly-2010: Jul-26 to Aug-06 to biweekly-2010: Aug-09 to Aug-20

comment:6 Changed 2010-08-23T12:07:18-05:00 by curtis

  • Milestone changed from biweekly-2010: Aug-09 to Aug-20 to biweekly-2010: Aug-23 to Sep-03

I updated to the latest codebase (FTK, ITK, and VTK), got FARSIGHT to compile, and updated the CMake cache files in the FTK codebase accordingly. Next, I need to make some updates to the bf-itk project. Then I can take some screenshots documenting how Bio-Formats works in the FARSIGHT tools.

comment:7 Changed 2010-08-24T14:39:16-05:00 by curtis

See also ticket #169.

comment:8 Changed 2010-09-17T17:50:22-05:00 by curtis

  • Owner changed from curtis to hiner
  • Status changed from accepted to assigned
  • Milestone changed from biweekly-2010: Sep-07 to Sep-17 to biweekly-2010: Sep-20 to Oct-01

comment:9 Changed 2010-09-22T13:15:28-05:00 by curtis

  • Owner changed from hiner to hinerm

comment:10 Changed 2010-10-12T09:08:26-05:00 by hinerm

  • Status changed from assigned to accepted

comment:11 Changed 2011-01-14T15:14:21-06:00 by hinerm

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

Step-by-step tutorials with images documenting the use of Bio-Formats with FARSIGHT modules (Nucleus Editor and Trace Editor) can now be found here:
 http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats

The main limitation found concerns FARSIGHT, in that images must have an 8-bit unsigned pixel type. This was documented in ticket 246.