Cellpose 0.6.5-foss-2020b

There is a newer version of Cellpose

a generalist algorithm for cellular segmentation

Accessing Cellpose 0.6.5-foss-2020b

To load the module for Cellpose 0.6.5-foss-2020b please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load Cellpose/0.6.5-foss-2020b

There is a GPU enabled version of this module: Cellpose 0.6.5-fosscuda-2020b

BEAR Apps Version

2020b

Architectures

EL8-cascadelakeEL8-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 Cloud and CaStLeS 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 0.6.5
  • natsort 7.1.1
  • pyqtgraph 0.12.2
  • tifffile 2021.8.8

More Information

For more information visit the Cellpose website.

Dependencies

This version of Cellpose has a direct dependency on: foss/2020b numba/0.53.1-foss-2020b OpenCV/4.5.1-foss-2020b-contrib PyQt5/5.15.1-GCCcore-10.2.0 Python/3.8.6-GCCcore-10.2.0 PyTorch/1.7.1-foss-2020b tqdm/4.56.2-GCCcore-10.2.0

Other Versions

These versions of Cellpose are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 11th August 2021