One you have cloned the repository and set up the environment, you can launch the interface.

Launching the Interface

1. In VS Code, open the gui.py file inside the caiman_gui folder.

2. Click the Run (▶️) button at the top to start the program.

   

3. After a few seconds, the GUI window will appear.

   

4. The default model is Calcium. To switch to Voltage, go to the Model tab at the top of the CaImAn Analyzer window and select Voltage.

5. In the input folder box, enter the path to the folder containing the TIFF files to analyze.

6. In the output folder box, enter the path where results should be saved.

7. Click Run Model to start the analysis.

Calculating Variables

Frame Rate (frames per second):

1. Open one of your CZI files in ImageJ/Fiji.

2. Search for Info in the search bar and run it.

3. Scroll until you find Frame Interval.

4. Calculate frame rate as:

   Frame Rate = 1 / Frame Interval
   

   Example:

   1 / 0.00251 = 398 FPS
   

5. Enter this value into the Frame Rate field in the GUI Parameters box.

Dxy (spatial resolution in µm per pixel):

1. Open a CZI file in ImageJ/Fiji.