Step 2 : Save storenames using Storenames GUI - LernerLab/GuPPy GitHub Wiki

a. Click on Open Storenames GUI. A separate 'Storenames GUI' window will pop up in a new tab for each folder selected for analysis. Save Storenames in all the windows as described in the next steps.

b. On the left, the folder name is displayed along with some basic instructions to save the storenames. Available storenames within the folder are auto-populated in a list. You need to select which of these storenames are to be analyzed from this folder

  • if you used TDT Synapse to record data, these are the storenames you named in Synapse
  • if you used 'csv' files as the input, the storenames are the names of the csv files you provided
  • if you used Neurophotometrics to record data, this step will read the data and convert them to different csv files and the storenames are the names of those new csv files.
  • if you used Doric system to record data, this step will read the csv file or .doric files and the storenames are the names of column names or key names in case of .doric files.

c. Select all the relevant storenames for analysis by adding them to the list on the right using the '>>' button. Add the storenames for all your fiber photometry data (signal and control channels) and for any timestamps you want to use for making PSTHs.

d. Click 'Select Storenames' to populate the 'Selected Storenames' window below.

e. Follow the example provided in the instructions on the left to enter more interpretable names for your storenames. Note: You must name your signal and control channels consistently for the analysis to work properly, following the naming conventions noted in the instructions on the left. Timestamps can be saved using any convention.

  • Storenames GUI has been designed to make sure user follow naming convention and user does not make many errors in the process.
  • After your first use, GuPPy will remember your choices for previous saved storenames and generate a pop up menu to easily reselect them.
  • If user wants to delete those previous choices which GuPPy has stored before, execute the following command in a new terminal window.
rm .storesList.json
  • Close the storenames pop-up when you are done with it.

Note: There may be instances where you want to use a specific storename more than once. If that is the case:

  • There is a checkbox named 'Storenames to repeat'. When you check the checkbox, a new widget with two options as shown below will pop up alt-text
  • At the top in the widget box, there is a bar named 'Select Storenames which you want more than once'. When you click that bar, a drop down menu will appear with all of the storenames from your collected data
  • Select the specific storename(s) that you want to use more than once
  • Below this bar, there is another bar named 'Number of times you want the above storename'
  • Write in the number of times you want to repeat the storename(s)
  • Here is an example scenario: let's say I have the storenames Dv1A, Dv2A, Dv3A. For this data, Dv1A represents the isosbestic control while Dv2A and Dv3A represent signal data from one brain area that has two different fluorescent indicators (ex dLight and RCaMP). Now, I want to treat Dv1A as my control channel for both Dv2A and Dv3A. Below is how I would save the storenames for this scenario:
{"storenames": ["Dv1A", "Dv2A", 
                "Dv3A", "Dv1A"], 
"names_for_storenames": ["control_DA", "signal_DA", 
                         "signal_RCAMP", "control_RCAMP", 
                         ]}

f. Select whether you are creating a new storeslist file or need to overwrite a previous file (for re-analysis).

g. Save by clicking 'Save' at the bottom of the window. After clicking save, the GUI window will look like the screenshot below, populating the 'Location to Stores List file' field.

alt-text

i. Close the Open Storenames GUI window, returning to the window where you entered input parameters.