David Gault

MatLab: Bfopen preallocating cell of wrong size

2

Issue was raised by a user on forum thread https://forum.image.sc/t/bfopen-in-matlab-preallocates-a-cell-variable-of-the-wrong-size/72045 In the below line of `bfopen` in the matlab toolbox the cell size is being allocated with `colorMaps = cell(numImages);...

SVS: IndexOutOfBoundsException when opening lower resolutions

1

Issue was raised on forum thread https://forum.image.sc/t/cannot-import-svs-file-using-bioformats/71840 A sample file reproducing the issue can be found at [GDC](https://portal.gdc.cancer.gov/files/fc037dde-4333-4ab7-b3a9-2b596cd16799) (tested with BF 6.10.1) ``` Exception in thread "BioFormats-ThumbLoader" java.lang.IndexOutOfBoundsException: Index: 0,...

LIF: ArrayIndexOutOfBoundsException when parsing offsets

3

Issue was raised via [QA-31234](https://www.openmicroscopy.org/qa2/qa/feedback/31234/) and a sample file was provided. Testing the sample file with Bio-Formats 6.10.1 was able to reproduce the same issue as described in the report....

ND2: Invalid XML characters

5

Issue was raised on forum thread https://forum.image.sc/t/bfconvert-invalid-xml-character-unicode-0xffff-for-nd2-file/40453/3 and sample files have been provided in QA-29424 The issue was reproduced as described using Bio-Formats 6.5.1. To reproduce, run `showinf -nopix -omexml`...

Imspector MSR: NumberFormatException when parsing timepoints

4

This issue was raised on Imagesc thread https://forum.image.sc/t/msr-files-in-bio-formats/90582 and a sample file was provided at https://zenodo.org/records/10476252?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6IjQ1ODRiNjkwLWExNTUtNGJlZS1hYjJhLTNjOTgzZWRiNmUwZCIsImRhdGEiOnt9LCJyYW5kb20iOiJhZjI1M2JjZDc4Y2Q5ZjE0MzhiMTZhOWQwMWRkYWQ2ZiJ9.Xz8eb6cxS-jWu5GvAnYEqkKlFzjLNoYYc3bI3mjtci7tinEdRZIvj8CjTyHqTNJj1waBVpaNJZvK8IvN0y3Y0g Using the provided sample file the issue can be reproduced with Bio-Formats 7.1.0 The...

VirtualImagePlus: Retain B&C settings for each slice

4

This is a follow up to a previous PR https://github.com/ome/bioformats/pull/3850/files and is an attempt to address the issues raised in https://forum.image.sc/t/b-c-for-a-whole-virtual-stack-cont/57811/10 The fix here reapplies the table settings for each...

CZI: Autostich fails

10

Issue was raised on forum thread https://forum.image.sc/t/zoom-from-overview-to-detailed-scan-for-imported-czi-files/85002/6 A sample was provided that reproduces the issue with Bio-Formats 7.0.0 - https://zenodo.org/record/8423633 When opening the file, even with the autostitch option selected,...

bfconvert: Using channel option does not remove additional channel elements from OME-XML

1

Issue was reported on forum thread https://forum.image.sc/t/extracting-a-single-channel-using-bfconvert/91632 The original error was reported when trying to read using AICSImage resulted in the error: ``` ValueError: conflicting sizes for dimension 'C': length...

native-lib-loader: UnsatisfiedLinkError when calling library is in a different classloader

1

This issue was raised on forum thread https://forum.image.sc/t/issue-with-ikvm-and-native-lib-loader-in-bioformats-in-net/90082 The problem was seen by the Bio-Formats .NET project in [this issue](https://github.com/BiologyTools/BioFormatsNET6/issues/3) when using IKVM Maven SDK instead of ikvmc.exe A detailed...

Slidebook: ArrayIndexOutOfBoundsException

6

Issue was reported on QA-33754, import failure during an OMERO workshop. `Server name: workshop.openmicroscopy.org, version: 5.6.6` The failure looks to be due to no pixelOffsets being found resulting in much...