Batch analysis: traces - galizia-lab/pyview GitHub Wiki

With this, we have seen the output options for overviews and movies. Now: export traces.

We have manually looked at traces in VIEW. They are based on the ROIs that were selected and saved in ILTIS.

To save traces, use the template program 06_PROGS/export_traces_synthetic.py.

The syntax is very similar to what we described above for movies:

• You need a list of animals to be considered.
• You need to label, within the list file in column “Analyze”, every row with a number that creates subgroups (if needed)
• With the variable Analyze_column_values_to_use in export_traces_synthetic.py, define which values to consider.

As a result, you will obtain a file in a subfolder of 04_OUTPUT, subfolder with the name of the animal, name here: Synthetic_data_strip/Synthetic_data_strip.gloDatamix.csv.

This csv file fills the first columns with all information from the .list file, and the information about the ROI used in each row. In addition, there is a column with the CTV value, as calculated with the CTV chosen, here: CTV 22, taking the difference between frame 45 (average 44-46) and frame 25 (average 24-26). The right columns contain the time-traces.

These files can be loaded in a statistics program to analyze data statistically, or to use other graphics programs to display the traces.

Let’s look at the right columns:

Playing with the traces file in Excel:

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