There is a newer version of python-bioformatsPython-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-2019b-Python-3.7.4
To load the module for python-bioformats 4.0.0-foss-2019b-Python-3.7.4 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load python-bioformats/4.0.0-foss-2019b-Python-3.7.4
There is a GPU enabled version of this module: python-bioformats 4.0.0-fosscuda-2019b-Python-3.7.4
BEAR Apps Version
EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
- boto3 1.15.9
- botocore 1.18.9
- Cython 0.29.14
- future 0.18.2
- jmespath 0.10.0
- numpy 1.18.2
- s3transfer 0.3.3
For more information visit the python-bioformats website.
This version of python-bioformats has a direct dependency on: foss/2019b Java/11 Python/3.7.4-GCCcore-8.3.0 SciPy-bundle/2019.10-foss-2019b-Python-3.7.4
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 19th October 2020