bioio-devs / bioio-bioformats

A BioIO reader plugin for reading bioformats formatted images.

bioio-bioformats

A BioIO reader plugin for reading many file formats like as seen here using bioformats

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Documentation

See the full documentation on our GitHub pages site - 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

Installation

Stable Release: pip install bioio-bioformats
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.

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 or check this repository's issue tab.

Development

See CONTRIBUTING.md for information related to developing the code.