A BioIO reader for reading bioformats formatted images.
Project description
bioio-bioformats
A BioIO reader plugin for reading many file formats like as seen here using bioformats
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.
Project details
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