Covert lab pipeline to analyze the fluorescent live-cell imaging data. For filtering/visualization of the results, see covertrace.
Operations will be generated by feeding input arguments into SettingUpCaller.
+----------------------------+
| Settingup operations |
+-------------+--------------+
|
| setting.json
v
+----------------------------+
| Preprocessing operations |
+-------------+--------------+
|
| images in processed/
v
+----------------------------+
| Segmentation operations |
+-------------+--------------+
|
| uint16 labels in segmented/
v
+----------------------------+
| Tracking operations |
+-------------+--------------+
|
| uint16 labels in tracked/
v
+----------------------------+
| Postprocessing operations |
+-------------+--------------+
| ini_df.npz
| uint16 labels in objects/
| +----------------------------+
+------------------------->| Subdetection operations |
| +-------------+--------------+
v |
+----------------------------+ | uint16 labels in objects/
| ApplyObjects | <----------------------+
+-------------+--------------+
|
| df.npz
v
Covertrace
git clone https://github.com/braysia/covertrack.git
cd covertrack
python setup.py install
imagemagick is required.
For futher details see here.
cat requirements.txt | xargs -n 1 pip install
For a quick run, run ./tests/tests.sh.
The results will be written in tests/output/testimages/. Check images in tests/output/testimages/objects to see how segmentation and tracking worked.
To do a test run for bigger images, run ./tests/tests2.sh. The results will be stored in tests/output/testimages2/.
covertrack input_file/input_tests1.py
See covertrack --help for more options.
See input_file directory for examples of input arguments.
Or see HOW_TO_WRITE_INPUT_FILE.