QuimP_to_AmoePy_bridge

Simple notebok for converting QuimP segmented cell contours to a format that can be imported into Amoepy for downstream analysis of cell morphology over time.

TODO

• Write instructions to get the sname.csv file from QuimP
• Write instructions to run notebook
• Make notebook available on Colab (?)
• Set up COLAb so that notebook can be run and edited but not save changes (?)
• Add a description of the different snake data types
• Add example snake.csv file for testing
• Add option to run on entire directory and save each file individually (?)

How to use this tool?

You first need to convert the .QCONF file containing all the data from the analysis in QuimP into a _snake.csv file:

1. Open the QuimP BAR in Fiji
2. Select the Format Converter plugin

3. Load the .QCONF file containing the contour analysis using the Load QCONF button.

4. Select snakes and make sure to unselect File per frame, so that it reads File per cell.

5. You will end up with a _snake.csv file for each cell detected in your analysis.

File formats

The _snake.csv is a TAB-sepparated file with the following structure:

In order to be able to be imported into AmoePy, the snake contour coordinates need to be converted into a .txt file with the following format:

Running the notebook

The conversion notebook is also available in Google Colab