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replace AllenCellModeling with bioio-devs #26

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replace AllenCellModeling with bioio-devs
toloudis Mar 16, 2026
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fixup readme to refer to bioio
toloudis Mar 18, 2026
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21 changes: 11 additions & 10 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# czi-to-ome-xslt

[![Build Status](https://github.com/AllenCellModeling/czi-to-ome-xslt/workflows/Test%20Main/badge.svg)](https://github.com/AllenCellModeling/czi-to-ome-xslt/actions/test-main.yml)
[![Build Status](https://github.com/bioio-devs/czi-to-ome-xslt/workflows/Test%20Main/badge.svg)](https://github.com/bioio-devs/czi-to-ome-xslt/actions/test-main.yml)

XSLT files to convert from CZI (Zeiss) microscopy image metadata
to OME image metadata schema.
Expand All @@ -13,7 +13,7 @@ If you want to use this work in a standalone fashion we recommend submoduling
this repository into your own repo:

```bash
git submodule add https://github.com/AllenCellModeling/czi-to-ome-xslt.git
git submodule add https://github.com/bioio-devs/czi-to-ome-xslt.git
```

You can then run the transformation in any language of your choosing.
Expand All @@ -40,28 +40,32 @@ with open("your-converted-czi-metadata.ome.xml", "w") as open_f:
open_f.write(str(omexml))
```

This work has already been incorporated into
[`aicsimageio`](https://github.com/AllenCellModeling/aicsimageio).
This work is incorporated into
[`bioio`](https://github.com/bioio-devs/bioio), in the [`bioio-czi`](https://github.com/bioio-devs/bioio-czi) module.

```python
from aicsimageio import AICSImage
from bioio import BioImage

img = AICSImage("your-file.czi")
img = BioImage("your-file.czi")
img.ome_metadata
```

## EXSLT

This work utilizes the EXSLT extensions for XSLT 1.0 (for example, the `str:tokenize` function). Popular XML libraries
such as `lxml` have built in support for EXSLT. To use these extensions, include the necessary attributes on `<xsl:stylesheet>` in the
file you are working on:

```
<xsl:stylesheet version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:ome="http://www.openmicroscopy.org/Schemas/OME/2016-06"
xmlns:str="http://exslt.org/strings" extension-element-prefixes="str">
...
```

You can then use an EXSLT function like so:

```
<xsl:value-of select="str:tokenize(/Some/Path, ',')" />
```
Expand All @@ -73,7 +77,6 @@ For more information on using EXSLT and the functions avaialbe, see the [EXSLT d
For full metadata comparison between XSLT and Bioformats, see
[comparison](./docs/comparison).


## Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit
Expand All @@ -88,8 +91,6 @@ than Python**.
For instructions on how to contribute new additions to the XSLT and/or tests, see
[CONTRIBUTING](./docs/CONTRIBUTING.md).


---


***Free software: BSD license***
**_Free software: BSD license_**
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