quickstart / tl;dr
SSAM-lite is an easy to use a lightweight web browser application to identify cell types in single-molecule spatial transcriptomic data such as MERFISH, SEQfish, ISS/CARTANA, osmFISH, etc. This quickstart guide is for you if you have
very little time,
an understanding of SSAM,
or just want to get a quick glance at what SSAM-lite can do.
Otherwise we would recommend that you have a look at the user guide.
Test data
Download the test data from Zenodo (https://zenodo.org/record/5517606) and unzip it.
Open SSAM-lite
Enter https://ssam-lite.bihealth.org in the address bar of your favourite web browser.
My first analysis
Click on “Get going!”
You are in the Data Center now. Click on “Coordinates” and select the coordinates.csv from the Codeluppi_osmFISH directory in the test data. Do the same for the “Signatures” (obviously use the signature.csv from the same directory this time, duh!)
In the Parameters section leave the pixel width at its default, set the KDE kernel bandwidth to 5 and the expression threshold to 50.
The time is flying by so we head straight for Analysis without any further explanation and click on “Run Kernel Density Estimation”. Time for a short break now, this step might take a few seconds.
When the KDE has been estimated scroll further down and hit “Infer Cell Types”.
As last step adjust the color palette by clicking the “Custom color map” button and selecting the custom_colors.csv.
Done!
That’s how easy SSAM-lite is!