mkcor / repro-tgmm

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

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 [e-mail]
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 [e-mail]:~/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