Skip to main content


Project description

SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation)

Author: Jeongbin Park (\ :sup:1,2 and Wonyl Choi (\ :sup:3

:sup:1\ Digital Health Center, Berlin Institute of Health (BIH) and Charité – Universitätsmedizin, Berlin, Germany; :sup:2\ Faculty of Biosciences, Heidelberg University, Heidelberg, Germany; :sup:3\ Department of Computer Science, Boston University, Boston, the United States of America

(Not referring this :laughing::

This project was done under supervision of Dr. Naveed Ishaque ( and Prof. Roland Eils (, and in collaboration with the SpaceTx consortium and the Human Cell Atlas project.

Please also check our example Jupyter notebooks here:


Currently SSAM was only tested with Python 3 in Linux environment. In addition to this package, SSAM requires a local R installation with pre-installed packages feather and sctransform. For details, please follow the instructions here:




J Park, W Choi, S Tiesmeyer, B Long, LE Borm, E Garren, TN Nguyen, S Codeluppi, M Schlesner, B Tasic, R Eils, N Ishaque. "Segmentation-free inference of cell types from in situ transcriptomics data." bioRxiv 800748. doi:


Copyright (C) 2018 Jeongbin Park and Wonyl Choi

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

ssam-1.0.2.tar.gz (26.3 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page