Track axon growth cones in video data

Clone the repo:

git clone --recursive https://github.com/LoaloaF/axtrack.git && cd axtrack

Create anaconda env and install the submodules:

conda env create --file axtr.yml
conda activate axtr
cd libmot && python setup.py install develop --user
cd ../pyastar2d && python setup.py install develop --user && cd ../

Download model & example data:

curl https://polybox.ethz.ch/index.php/s/Run8gaUVT45hmjX/download > deployed_model/E1000.pth
curl https://polybox.ethz.ch/index.php/s/qlOKY3asRdcnmKh/download > examples/example_timelapse.tif

Run the included example:
python example/test.py

The example goes through the three simple steps of tracking axons in a 3D-grayscale-tif file.

import axtrack

# first setup the directories for reading and writing data
parameters, model, stnd_scaler = axtrack.setup_inference(dest_dir)

# create the input data object
timelapse = axtrack.prepare_input_data(imseq_fname, parameters, dest_dir, inference_data_dir,
                            stnd_scaler, mask_fname=mask_fname, use_cached_datasets=use_cached_datasets, 
                            check_preproc=check_preproc, input_metadata=input_metadata)

# get axon detections
axon_dets = axtrack.inference(timelapse, model, dest_dir, parameters, 
                                detections_cache=cache_detections,
                                astar_paths_cache=astar_paths_cache,
                                assigedIDs_cache=assigedIDs_cache)

dets = axon_dets.IDed_dets_all

test.py should create the video below.

To improve performance on your dataset you may consider labelling a subset of your data and retraining the model. To do this, label a timelapse using the jupyter notebooks in ./data_prep_nbs/. Then, train on your data by running ./experiment/experiment.py.

AxTrack is distributed under the MIT license:

Copyright 2022 Simon Steffens

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.