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README.md

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covertrack

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

Installation

git clone https://github.com/braysia/covertrack.git
cd covertrack
python setup.py install

imagemagick is required.
For futher details see here.

Test

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/.

Examples

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.