SpikeIt

Quick User Manual

Upload the trace tables which where generated using the FIJI-plugin

Check parameters stringency and dF/F threshold in the section Plot Curves

Once you are happy with the parameters, click on 'Start Analysis' and wait till all tables are processed

After the Analysis ran on all tables, you can view the results and export the results-tables in the Export-Section

Sample Info

Preview Tables

Table Preview

Plot Calcium Traces

Plotting Parameters

Use Facet Grids to display single traces

Show Peak Points (Start in Red, End in Blue)

Download Plot

Plot-Width in cm

Plot-Height in cm

Download Plot

Export Data Tables

Save as

Select a Table

Download Table

Plot Results

Select which Parameters to Plot

Inspect Tables

Select a Table

Download the Fiji-plugin script

Here you can download the Fiji-plugin script used to extract the values from Calcium-imaging videos. After downloading, drag the Python-script into the Fiji-Toolbar. The Fiji-script Editor should pop up now. Click on Run, select the folder with your videos and determine a radius for the cell selections. After setting the parameters, click on the center of every cell you want to measure. After the script is done, you should find a new folder with the measurement tables in same directory with your videos. You can analyze those tables using this ShinyApp. Happy Spiking!

Download Fiji Plugin

About

This ShinyApp was developed to streamline calcium imaging experiments in the Schratt Lab.

Source Code can be found on our Github-repo