Spatial Sequencing Analysis Pipeline.

SSAM-lite is a complete spatial sequencing analysis pipeline that runs entirely in your browser.

Tutorial Get going!

Data Center

Click or drag-and-drop to upload your data.


Parameters

Use previews to find an optimal set of parameters for your analysis.

Use preview generator for parameter search
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Analysis

Step 1: Kernel Density Estimation

As a first step, we run a KDE that creates a density of mRNA expression.

Run Kernel Density Estimation

Step 2: Cell Assignments

We can now infer cell types.

Infer Cell Types

Clear analysis

About

The SSAM framework was conceived by Dr. Jeongbin Park as part of his PhD project at the Berlin Institute of Health. Read the original SSAM publication to learn more about the methods.
SSAM-lite has been designed and implemented by Sebastian Tiesmeyer at the Berlin Institute of Health. Learn more about SSAM-lite here.
For a comprehensive documentation of the SSAM-lite tool check out our Read the Docs page.
If you are using SSAM-lite for your research please cite:
Tiesmeyer S, et al. 2021. SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data. bioRxiv. doi: 10.1101/2021.09.29.462194
© 2021 Sebastian Tiesmeyer, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité -