https://github.com/jni/pia-tracking

Scripts to work with Pia Larsson's platelet tracking data
https://github.com/jni/pia-tracking

Last synced: about 1 month ago
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Scripts to work with Pia Larsson's platelet tracking data

• Host: GitHub
• URL: https://github.com/jni/pia-tracking
• Owner: jni
• License: bsd-3-clause
• Created: 2020-09-14T03:04:07.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2021-10-21T07:27:08.000Z (about 3 years ago)
• Last Synced: 2024-10-05T00:31:04.908Z (about 2 months ago)
• Language: Python
• Size: 5.3 MB
• Stars: 4
• Watchers: 6
• Forks: 0
• Open Issues: 13
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# Scripts/notebooks to segment and track platelets in a growing thrombus

Current files:

- `fl.py` contains some utilities used in the notebooks, including objects for

  opening the ND2 file and keeping track of various processed data products

  (smoothing, thresholding, segmentation, etc.)

- The "process images" notebook is the first step, goes from images to

  segmentation. It creates output files in a timestamped subfolder of the

  current working directory.

- The "define variables" notebook then uses that segmentation to create tracks.

Goals:

- turn this from a set of loosely tied notebooks to a command-line utility that

  runs various parts of the pipeline

- use zarr to save the original data and intermediate products

- use dask for processing where possible

- get the tracks into the napari tracks layer from napari/napari#1361

---

Installation:

```bash

git clone https://github.com/jni/pia-tracking.git

cd pia-tracking

conda env create -f environment.yml

conda activate platelet-tracking

```