PyImageJ 1.3.1-foss-2021a

PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.

Accessing PyImageJ 1.3.1-foss-2021a

To load the module for PyImageJ 1.3.1-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load PyImageJ/1.3.1-foss-2021a

BEAR Apps Version




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.


  • imglyb 2.0.1
  • jgo 1.0.5
  • JPype1 1.4.1
  • labeling 0.1.13
  • PyImageJ 1.3.1
  • scyjava 1.8.1
  • setuptools 61.3.1

More Information

For more information visit the PyImageJ website.


This version of PyImageJ has a direct dependency on: foss/2021a Java/11 matplotlib/3.4.2-foss-2021a Maven/3.6.3 Pillow/8.2.0-GCCcore-10.3.0 Python/3.9.5-GCCcore-10.3.0 scikit-image/0.18.3-foss-2021a SciPy-bundle/2021.05-foss-2021a xarray/0.19.0-foss-2021a

Last modified on 29th November 2022