Unsupported: Use of this version of python-bioformats is not supported. More information on our Applications Support and Retention Policy.Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. Python-bioformats uses the python-javabridge to start a Java virtual machine from Python and interact with it. Python-bioformats was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org).
Accessing python-bioformats 4.0.0-foss-2020a-Python-3.8.2
To load the module for python-bioformats 4.0.0-foss-2020a-Python-3.8.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load bear-apps-unsupported/handbuilt/2019
module load python-bioformats/4.0.0-foss-2020a-Python-3.8.2
BEAR Apps Version
- boto3 1.15.9
- botocore 1.18.9
- jmespath 0.10.0
- s3transfer 0.3.3
For more information visit the python-bioformats website.
This version of python-bioformats has a direct dependency on: foss/2020a Java/11 Python/3.8.2-GCCcore-9.3.0 SciPy-bundle/2020.03-foss-2020a-Python-3.8.2
These versions of python-bioformats are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
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Last modified on 2nd October 2020