https://github.com/mkcor/repro-tgmm

Reproduce segmentation results from open research in live imaging of mouse embryonic development at the single-cell level.
https://github.com/mkcor/repro-tgmm

Last synced: 4 months ago
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Reproduce segmentation results from open research in live imaging of mouse embryonic development at the single-cell level.

• Host: GitHub
• URL: https://github.com/mkcor/repro-tgmm
• Owner: mkcor
• License: bsd-3-clause
• Created: 2024-05-17T13:58:52.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2024-08-27T13:52:04.000Z (almost 2 years ago)
• Last Synced: 2025-02-21T12:44:55.610Z (over 1 year ago)
• Language: HTML
• Size: 2.21 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# repro-tgmm

Reproduce segmentation results from open research in live imaging of mouse embryonic development at the single-cell level.

## Create (remote) computing environments

    mkdir -p ~/envs

    python3.9 -m venv ~/envs/load

    source ~/envs/load/bin/activate

    pip install --upgrade pip

    pip install -r requirements/load.txt

    deactivate

    python3.9 -m venv ~/envs/proc

    source ~/envs/proc/bin/activate

    pip install --upgrade pip

    pip install -r requirements/proc.txt

    deactivate

## Create (local) viewing environments

    mkdir -p ~/envs

    python3.11 -m venv ~/envs/view

    source ~/envs/view/bin/activate

    pip install --upgrade pip

    pip install -r requirements/view.txt

    deactivate

    python3.9 -m venv ~/envs/pres

    source ~/envs/pres/bin/activate

    pip install --upgrade pip

    pip install -r requirements/pres.txt

    deactivate

## Workflow

    ssh mkcor@broome.cluster.recurse.com

    cd repro-tgmm/

    cd data/

    cat README.md  # how to download the bioimaging data

    source ~/envs/load/bin/activate

    python load/read_write.py .  # convert data to zarr and save sample

    deactivate

    source ~/envs/proc/bin/activate

    python proc/run_3d_segmentation_embryo.py .  # process data

    deactivate

    cd tgmm/

    /home/mkcor/tgmm-paper/install/bin/ProcessStack_woGPU config.md 184

    /home/mkcor/tgmm-paper/install/bin/ProcessStack_woGPU ../data/outputs/sample_frame_184_seg_conn74_rad2.bin 14 14

    cd ../

    source ~/envs/load/bin/activate

    python load/save_tgmm_seg.py .  # save result from reproducibility

    deactivate

    logout

    scp mkcor@broome.cluster.recurse.com:~/repro-tgmm/data/outputs/*.npz view/.

    source ~/envs/view/bin/activate

    cd view/

    python explore_seg_results.py  # compare segmentation results in napari

    deactivate

## References

McDole K, Guignard L, Amat F, Berger A, Malandain G, Royer LA, Turaga SC,

Branson K, Keller PJ (2018) "*In Toto* Imaging and Reconstruction of

Post-Implantation Mouse Development at the Single-Cell Level" Cell,

175(3):859-876.e33.

DOI: [10.1016/j.cell.2018.09.031](http://doi.org/10.1016/j.cell.2018.09.031)