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Hi,
I realised a pretty significant bug in the Zeiss Lightsheet CZI reader. It does read the sizes of the individual stacks wrongly (assumes the biggest stack size for all of them), which is a huge p…
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**To Reproduce**
Steps to reproduce the behavior:
1. Go to https://frontend.cryoet.staging.si.czi.technology/datasets/10003?metadata=dataset&tab=metadata
2. Click on View All Data
3. Notice Organi…
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Hi,
I have a CZI that does open correctly with BioFormats 6.1.1. I did the following
- open compressed CZI in Fiji
- open uncompressed CZI in Fiji
- export CZI as OME-TIFF from ZEN and open in…
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I would need a minimal CZI or ND2 or LIF file that contains:
- 2 channels
- 2 z-slices
- 2 timepoints
I could also be more than 2 for each dimensions, but it should also be so **small** that w…
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Tiles get scrambled at random when importing 2d images from czi. If czi has multiple channels, all the channels in the tile are scrambled. Following code used to import czi and write nrrd files for ea…
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I'm excited about using BigStitcher (particularly shading correction which I had hacked in to your previous stitching plugin). However, I'm running into the following problem...
I have a single cz…
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## Background
I'm attempting to use ASHLAR 1.15.2 on a couple Zeiss (CZI) 5-channel whole slide images. However, the results are showing strange tiling issues, basically sparse tiles with no data in …
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Currently, SCIFIO (and therefore _Image Reader_ in KNIME) opens only the first series when a multi-series czi file is opened. (Tested in Fiji with SCIFIO enabled, and in KNIME).
When importing with B…
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PIMS Bioformats has compatibility with nd2 files AND czi files. Refer to note [in the PIMS source](https://github.com/soft-matter/pims/blob/5bbe33376d0fdd15318af65c591d66608e8e7a1e/pims/api.py#L111) t…
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This issue was first reported in https://forum.image.sc/t/czi-reader-illuminationtype-mapping-and-exposuretime-units/37557/3 and a sample file showing the issue is available in QA-29273
In the samp…