David Gault

Leica LIF: Missing laser settings

9

Issue was raised on forum thread https://forum.image.sc/t/leica-lif-metadata-fiji-extracting-laser-settings-for-multiple-channels/34250/4 Device information is correctly populated on OME-XML However additional metadata such as laser intensity shown in 'Show Info' only contains values for a...

ND2: IllegalArgumentException: 0 must be non-null and strictly positive

10

This issue was raised on the thread https://forum.image.sc/t/exception-issue-when-opening-nd2-files-with-bio-formats/40462 A sample file has been provided in QA-29421 and the exception is reproduced with Bio-Formats 6.5.1 From debugging the issue is caused...

ND2: Skewed image display

10

Image was raised on imagesc thread https://forum.image.sc/t/bfconvert-nd2-rgb-to-stack-of-tiff-grays-channels/48360/7 A sample file reproducing the issue with Bio-Formats 6.6.0 can be found at https://github.com/bioimage-analysis/Files/blob/bd6977bbfb5081ba74d6202b3faf5b92ae1529f2/error.nd2 Opening the file with Elements Viewer suggests that the...

Ventana BIF: Z stacks not supported

6

Issue was raised on imagesc thread https://forum.image.sc/t/qupath-not-opening-bif-z-stacks/50674 A sample file along with a related `tifp` file have been provided which reproduce the issue (tested with BF 6.6.1) Currently the sample...

Plugins: Add option for memoizer

6

Porting this from the original Trello card: https://trello.com/c/lYaGdkhX/203-investigate-using-memoizer-with-plugins Ideally this would include a configurable option to toggle the behaviour in the plugins settings

VSI: Cropped image due to incorrect offsets

1

Issue was raised on forum thread https://forum.image.sc/t/bio-formats-accidental-cropping-of-olympus-images/55689 and can be reproduced with the sample file provided. The dimensions read by Bio-Formats are correct however the image appears to be shifted...

BF Plugins: NPE when using Virtual Stack

1

Issue was reported on forum thread https://forum.image.sc/t/ome-tiff-issue-with-virtual-stack-java-nio-channels-closedchannelexception/66802 ``` java.lang.NullPointerException at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:459) at loci.formats.FormatReader.setId(FormatReader.java:1443) at loci.formats.in.OMETiffReader.initializeReader(OMETiffReader.java:1476) at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:368) at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:167) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at...

VSI: Inverted colours (RGB instead of BGR)

1

Issue was raised on forum thread https://forum.image.sc/t/qupath-0-3-2-inverts-colors-of-vsi-file/66609/3 A sample file was provided that reproduces the issue with Bio-Formats 6.9.1 The image appears to be detected by the reader as an...

VSI: incorrect exposure times

4

This issue was raised in forum thread https://forum.image.sc/t/bio-formats-exposure-time-incorrect-when-importing-vsi-files/46080 In the OME-XML the Exposure Time is the same for each plane. However the correct values can be found in the original...

VSI: Only part of image displayed

2

Issue was raised on forum thread https://forum.image.sc/t/importing-a-vsi-composite-image-in-imagej-via-bioformats-plugin-how-do-i-get-a-high-resolution-macro-image/35282/6 When opening the file the first series looks to have the correct dimensions but the image displayed is incorrect. The next series only...