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The `Immersion` enum does not have a value for silicone immersion. I'm using 'OTHER' at the moment, but I guess that Silicone could be have its own value. I found this missing while adding more ids fo…
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I have been trying to extract time stamps from a time-course image, but it has been giving me incorrect values. For example, using the ND2 file provided in this example [https://github.com/ome/bioform…
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### Description
Currently, HistoQC is using OpenSlide as WSI reader to manipulate whole-slide images. Unfortunately, OpenSlide is not really maintained anymore. It makes HistoQC only supports older f…
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See https://forum.image.sc/t/bad-reading-of-lif-metadata/73038 .
There is already a similar issue https://github.com/ome/bioformats/issues/3513 . Wasn't sure if it should there or a new issue. Just d…
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I have JPype 1.2.1 installed from conda-forge but I get the following warnings:
```
Bioformats.py:408: UserWarning: Due to an issue with JPype 0.6.0, reading is slower. Please consider upgrading JPy…
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I got a nd2 file with dimensions as slices(T) = 23, series(M) = 40 and frames(Z) = 11.
When I open this hyperstack image with Bio-format in FIJI, it did appears as 40 series. However, when I sele…
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I've been trying to use this library to read in a .jp2 image. However, the file is too big for it to handle. Bioformats has a solution for this under the open_bytes (?) function. How can I access this…
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If metadata is present as a filed called "metadata.txt", it is somehow read and this seems to cause a crash preventing any data to read.
Here is an example metadata.txt file causing such a crash:
[m…
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While working on https://github.com/IDR/idr0056-stojic-lncrnas/pull/1, @dominikl reported failures while applying the rendering settings:
````
Traceback (most recent call last):
File "/opt/omero…
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It seems that the image spacing information is not saved when using SCIFIO to save these formats.
I have written a small reader and writer that use SCIFIO, for test purposes:
https://github.com/fbud…