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Task #12205 (closed)

Opened 8 years ago

Closed 7 years ago

Last modified 7 years ago

ND2 Stage Positions

Reported by: jamoore Owned by: mlinkert
Priority: major Milestone: 5.0.3
Component: Bio-Formats Version: 5.0.1
Keywords: n.a. Cc: aaron.ponti@…, Erik.Welf@…, sbesson
Resources: n.a. Referenced By: https://trello.com/c/ArelsNBe/51-bug-nd2-bio-formats
References: n.a. Remaining Time: 0.0d
Sprint: n.a.


I have tried version 5.0.1 on a new ND2 file that has one additional dimension: stage positions (referred to as "X-Y" in the Nikon NIS software).

The file contains 4 stage positions each of which has 4 time points, 3 planes and 3 channels. In total, the file contains X/Y = 4 * T = 4 * Z = 3 * C = 3 = 144 images.

Bio-formats sees 5 series in the image, each of which has T = 4, Z = 3 and C = 3, for a grand total of 180 images.

The "virtual" 5th series recycles the images from the first one, although the indices are slightly out of phase. Please notice that if you want to use the NIS Viewer to check the file, it does not work correctly on the Mac.


Change History (5)

comment:1 Changed 7 years ago by sbesson

  • Cc Erik.Welf@… sbesson added

comment:2 Changed 7 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.0.3

comment:3 Changed 7 years ago by jamoore

comment:4 Changed 7 years ago by mlinkert

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

comment:5 Changed 7 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [3e522f2678de230bee3fb45ed7dfcd26eee940e1/bioformats.git] on branch develop) ND2: rework text annotation parsing so that dimensions are not overlooked

Fixes #12205.

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