Hsc 2025

[lufre1]

Update repo for HSC and add ex3:

ToDo

stardist cannot be tested at the moment (server down)

• test the following
  • micro-sam
  • synapse_net
  • cellpose
  • stardist
• exercise 3
  • 2d cell segmentation
    • with micro-sam / cellpose
  • 2d nucleus segmentation
    • with micro-sam
    • cellpose
    • stardist
  • 3d light microscopy segmentation
    • with micro-sam / cellpose
    • find fitting dataset (e.g. torch_em data?)
      owncloud-link
  • tracking
    • 2d cell segmentation with time
      • use micro-sam / cellpose for segmentation
      • use trackastra for actual tracking
    • reuse micro-sam sample data?

reviewed ex1 and ex2 and updated env_cpu.yaml

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[lufre1]

starting napari throws a depency error to snypase_net:

(hsc_course) [u17096@agq004 u17096]$ napari
[VGL] NOTICE: Replacing dlopen("libGL.so.1") with dlopen("libvglfaker.so")
[VGL] Shared memory segment ID for vglconfig: 1081351
[VGL] VirtualGL v3.1.2 64-bit (Build 20250106)
WARNING: Qt: Session management error: None of the authentication protocols specified are supported
16:18:47 : WARNING : MainThread : Qt: Session management error: None of the authentication protocols specified are supported
[VGL] Opening EGL device /dev/dri/card4
16:18:48 : ERROR : MainThread : napari.manifest -> 'synapse_net' could not be imported: Could not find file 'napari.yaml' in module 'synapse_net'

starting cellpose crashes

python -m cellpose

(cellpose) [u17096@agq003 dl-for-micro]$ python -m cellpose
Welcome to CellposeSAM, cellpose v
cellpose version: 4.0.4
platform: linux
python version: 3.11.12
torch version: 2.7.0+cu126! The neural network component of
CPSAM is much larger than in previous versions and CPU excution is slow.
We encourage users to use GPU/MPS if available.
GUI ERROR: No module named 'qtpy'
GUI FAILED: GUI dependencies may not be installed, to install, run
pip install 'cellpose[gui]'

stardist not in stardist-env

(stardist) [u17096@agq002 u17096]$ micromamba list | grep stardist
List of packages in environment: "/root/micromamba/envs/stardist"

[schilling40]

Thanks for the feedback! The issues should have been fixed.

Import of synapse-net should work.

Import of Cellpose works.

Stardist function throws warning but should work. Needs further testing.")
Import of Stardist function throws warning but should work. Needs further testing.