Cellpose 0.6.5-foss-2021a-CUDA-11.3.1

a generalist algorithm for cellular segmentation

Accessing Cellpose 0.6.5-foss-2021a-CUDA-11.3.1

To load the module for Cellpose 0.6.5-foss-2021a-CUDA-11.3.1 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load Cellpose/0.6.5-foss-2021a-CUDA-11.3.1

There is a CPU version of this module: Cellpose 0.6.5-foss-2021a

BEAR Apps Version

2021a

Architectures

EL8-haswell (GPUs: NVIDIA P100) — EL8-icelake (GPUs: NVIDIA A100, NVIDIA A30)

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 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: CUDA/11.3.1 foss/2021a numba/0.53.1-foss-2021a OpenCV/4.5.3-foss-2021a-CUDA-11.3.1-contrib PyQt5/5.15.4-GCCcore-10.3.0 Python/3.9.5-GCCcore-10.3.0 PyTorch/1.9.1-foss-2021a-CUDA-11.3.1-imkl tqdm/4.61.2-GCCcore-10.3.0

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 11th October 2021