Cellpose 2.2-foss-2022a

a generalist algorithm for cellular segmentation

Accessing Cellpose 2.2-foss-2022a

To load the module for Cellpose 2.2-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load Cellpose/2.2-foss-2022a

There is a GPU enabled version of this module: Cellpose 2.2-foss-2022a-CUDA-11.7.0

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake

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.

Extensions

  • Cellpose 2.2
  • fastremap 1.13.4
  • imagecodecs 2023.1.23
  • natsort 8.2.0
  • pyqtgraph 0.13.1
  • superqt 0.4.0
  • tifffile 2023.2.3

More Information

For more information visit the Cellpose website.

Dependencies

This version of Cellpose has a direct dependency on: foss/2022a numba/0.56.4-foss-2022a OpenCV/4.6.0-foss-2022a-contrib PyQt5/5.15.5-GCCcore-11.3.0 Python/3.10.4-GCCcore-11.3.0 PyTorch/1.12.1-foss-2022a QtPy/2.3.0-GCCcore-11.3.0 tqdm/4.64.0-GCCcore-11.3.0

Other Versions

These versions of Cellpose 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.

Last modified on 14th February 2023