Define experimental settings: create a .yml file - galizia-lab/pyview GitHub Wiki

An example for a .yml file is given in the file view_synthetic_666.yml in the folder synthetic_data. This file contains all flag settings. When working with PyView, you can change the flags interactively. When you have found flag values that are better suited for your data in PyView, you can save them to the .yml file from within PyView using a GUI button "Write flags to file". The file view/flags_and_metadata_definitions/view_flags_definition.csv in the repository contains all possible flag names that are used in PyView.

LE_loadExp: 666 defines that the data be synthetic. A value of “3” is data format “Till Photonics”. You can find all setup definition (i.e. readable data formats) in the file view/flags_and_metadata_definitions/setup_definitions.csv.

LE_CalcMethod: 3 defines that signals be calculated as deltaF/F. This method calculates relative changes in fluorescence, relative to the background which is defined as the average of frames LE_StartBackground: 4 to LE_PrestimEndBackground: 1. (Of course, you can change these numbers). LE_PrestimEndBackground is relative to the start of the stimulus, which is known from the column StimON in the list file.

STG_Datapath: 01_DATA defines where measurement data are stored. It is part of the philosophy of PyView that files in this folder are never touched or modified. (For synthetic data, that folder is empty).

STG_OdorInfoPath: 01_LISTS defines where the list files are to be found. Other flags define where results are to be stored. The folder structure defined by these flags is created when PyView is used, if those folders are not yet present. Other flags include which filters to be used, etc.

In this hands-on handbook we do not go through all flag settings: use the Wiki instead.

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