EtienneMueller / zebrafish_experiments

scripts and configs for running zebrafish experiments

zebrafish_experiments

scripts and configs for running zebrafish experiments

To Avoid conflicts

Update the dacapo.yaml file to point to your own mongodb and file storage path.

Organization:

├── configs  # everything related to data and dacapo configurations
│   ├── zebrafish  # ready to use dacapo config names including configs (architectures, datasplits, tasks, trainers, runs, predictions)
│   ├── scripts  # creation of dacapo configs
│   ├── yamls  # machine readable format for experiment configurations
├── scripts  # reusable cli scripts for common operations
├── scratch  # one-time scripts that aren't particularly reusable
├── runs  # logs from running training

installation

create conda environment with python >= 3.10

pip install git+https://github.com/funkelab/dacapo

pip install git+https://github.com/pattonw/funlib.show.neuroglancer@funlib-update

pip install -r requirements.txt

usage

use --help to get more info about script parameters

parsing spreadsheet

Data prep: data needs to be converted into n5s or zarrs for training. Once this is done you can use scratch/reformat_dataset.py to compute masks, sample points, etc. for the data.

creating dacapo configs

--force flag replaces the config in the mongodb with the new version. run configs contain copies of the configs that were used to create them so overwriting Task, Trainer, Architecture, and DataSplit configs won't affect old run configs.

1. python configs/scripts/datasplits/datasets.py update --force # getting very slow due to large number of resolution/target/dataset combinations
2. python configs/scripts/tasks/tasks.py update
3. python configs/scripts/trainers/trainers.py update --force
4. python configs/scripts/architectures/architectures.py update

creating a new run config

python configs/scripts/runs/runs.py update

running experiment

python scripts/submit.py run

logging

find logs in runs directory.

plotting

python scripts/plot.py plot

prediction

Single prediction from command line can be done using scripts/predict_daisy.

If you want to run multiple predictions and/or use a config file to have a record of what was run you can use python scripts/submit.py predict Example config files can be found in configs/zebrafish/predictions.

postprocessing

Postprocessing scripts can be found in scripts/post_processing. There are a couple versions for post processing workers. Post processing is broken down into 3 steps.

2. generate fragments (2: mwatershed or 1: waterz)
   • using 2 tends to do better but is slower and can generate many small fragments that slow down later processing
3. agglomerate fragments (2: mwatershed or 1: waterz)
   • using 2 utilizes long range affinities as well as short range affinities to generate more edges. Tends to do significantly better on datasets where false merges occur.
4. lut generation (2: mwatershed or 1: waterz)
   • 1 uses only positive edges to agglomerate and can be prone to agglomerating entire volumes into a single id. 2 uses mwatershed to run mutex watershed with negative edges and performs significantly better in cases where merge errors are an issue.