https://github.com/kaczmarj/quip-dots-to-cell-classification-data
Convert dotting labels on QuIP to training data for cell classification.
https://github.com/kaczmarj/quip-dots-to-cell-classification-data
Last synced: about 2 months ago
JSON representation
Convert dotting labels on QuIP to training data for cell classification.
- Host: GitHub
- URL: https://github.com/kaczmarj/quip-dots-to-cell-classification-data
- Owner: kaczmarj
- License: apache-2.0
- Created: 2021-08-16T19:33:12.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2021-08-25T17:44:27.000Z (almost 4 years ago)
- Last Synced: 2025-02-10T02:33:30.724Z (4 months ago)
- Language: Python
- Size: 550 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# convert quip to training data
Convert human dotting labels on QuIP to training data for cell classification task.
## example
```bash
python convert_quip_to_training_data.py \
--dump-path '/data/quip_distro/data/dump/TCGA:paad-2021-8-14-17-9-47' \
--svs-root /data/quip_distro/images/tcga_data/paad/ \
--polygon-root /data/quip_distro/data/kaczmarj/hou-scientific-data-nuclei-v0/paad_polygon/ \
--roi-name "Waqas 500p Non-Tumor 500p" \
--label-regex Waqas \
--subject-ids TCGA-2J-AABT \
--save-polygon-overlays \
--output-dir outputs
```
## convert output tiles to a movie
In the following example, we assume that the conversion script put its outputs in
a directory `outputs` and there is a class of labels called `lymphocytes`.
The `convert` command comes from ImageMagick, and to save to mp4, one must install
`ffmpeg`.
```bash
convert -delay 20 -loop 0 outputs/lymphocytes/*.png lymphocytes.mp4
```