semvec/pypi-packages huggingface dataset:
bioio-bioformats 1.3.2
A BioIO reader for reading bioformats formatted images.
License: MIT License
Requires Python: >=3.10

# bioio-bioformats

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A BioIO reader plugin for reading [many file formats like as seen here](https://docs.openmicroscopy.org/bio-formats/5.8.2/supported-formats.html) using `bioformats`

---


## Documentation

[See the full documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html) - the generic use and installation instructions there will work for this package.

Information about the base reader this package relies on can be found in the `bioio-base` repository [here](https://github.com/bioio-devs/bioio-base)

## Installation

**Stable Release:** `pip install bioio-bioformats`<br>
**Development Head:** `pip install git+https://github.com/bioio-devs/bioio-bioformats.git`

## Special Installation Instructions

**This package utilizes bioformats which depends on java**

To install java and maven with conda, run:

`conda install -c conda-forge scyjava`

You may need to deactivate/reactivate your environment after installing. If you are *still* getting a `JVMNotFoundException`, try setting `JAVA_HOME` as follows:

#### Mac / Linux
`export JAVA_HOME=$CONDA_PREFIX`

#### Windows
`set JAVA_HOME=%CONDA_PREFIX%\\Library`

## Example Usage (see full documentation for more examples)

Install bioio-bioformats alongside bioio:

`pip install bioio bioio-bioformats`


This example shows a simple use case for just accessing the pixel data of the image
by explicitly passing this `Reader` into the `BioImage`. Passing the `Reader` into
the `BioImage` instance is optional as `bioio` will automatically detect installed
plug-ins and auto-select the most recently installed plug-in that supports the file
passed in.
```python
from bioio import BioImage
import bioio_bioformats

img = BioImage("my_file.tiff", reader=bioio_bioformats.Reader)
img.data
```

## Issues
[_Click here to view all open issues in bioio-devs organization at once_](https://github.com/search?q=user%3Abioio-devs+is%3Aissue+is%3Aopen&type=issues&ref=advsearch) or check this repository's issue tab.


## Development

See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.