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Task #5114 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

BUG: Tile ordering is not correct for all .vsi files

Reported by: mlinkert Owned by: mlinkert
Priority: major Milestone: OMERO-Beta4.3.2
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: smithd@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-07-21 (1)

Description

Single-channel and 24-bit RGB files seem fine, but anything with multiple planes and/or multiple .ets files has subtle errors in the tile ordering.

It's not entirely clear how to detect or correct for this, as (near as I can tell) there is no tile index.

Change History (10)

comment:1 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [336062fc2289c5c84803c4acd4a91e0cf387e4e4/bioformats.git]) Lots of work on dimension detection and tile reading.

The cellSens reader now mostly works; closes #4156.
There are still a few wrinkles left to iron out though - see #5114.

comment:2 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [336062fc2289c5c84803c4acd4a91e0cf387e4e4/bioformats.git]) Lots of work on dimension detection and tile reading.

The cellSens reader now mostly works; closes #4156.
There are still a few wrinkles left to iron out though - see #5114.

comment:3 Changed 10 years ago by mlinkert

  • Cc smithd@… added

comment:4 Changed 10 years ago by mlinkert

  • Sprint changed from 2011-05-19 (12) to 2011-06-02 (13)

comment:5 Changed 10 years ago by mlinkert

  • Status changed from new to accepted

comment:6 Changed 10 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3 to OMERO-Beta4.3.1
  • Sprint 2011-06-02 (13) deleted

[e35079dc5e8457f5a2e762a9b4fca5c27128fde7/bioformats.git] fixes a few more problems here, so that in the case of multiple .ets files at least the first one will be read correctly. Datasets with multiple planes are still not correctly supported, though.

As mentioned previously, the solution to this problem is not obvious. So for 4.3, the plan is to release .vsi support with multi-plane datasets specifically not supported. We've been promised .vsi specifications from Olympus, so as soon as those arrive we will add proper support for multiple planes.

comment:7 Changed 10 years ago by mlinkert

  • Milestone changed from OMERO-Beta4.3.1 to OMERO-Beta4.3.2

comment:8 Changed 10 years ago by mlinkert

  • Remaining Time set to 1
  • Sprint set to 2011-07-21 (1)

We have now received sufficient documentation to fix this problem.

comment:9 Changed 10 years ago by Melissa Linkert <melissa@…>

  • Remaining Time changed from 1 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

comment:10 Changed 10 years ago by Melissa Linkert <melissa@…>

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