This directory contains configurations necessary for analyzing the public datasets from Deep profiling of mouse splenic architecture with CODEX multiplexed imaging (Goltsev et al. 2018).
The pipeline configured here will process the BALBc-1 sample and make the quantified cell data available through Cytokit Explorer and Cell Profiler Analyst (CPA).
A SQLite database will be generated at $OUTPUT_DIR/cytometry/cellprofiler/results and if the host (i.e. the machine running the Docker container) is not X11-enabled then there are several possible ways to use CPA given that the image paths (and others) written to the SQLite DB will all be based on the filesystem within the docker container. Some options are:
- Copy the data at
$OUTPUT_DIR/cytometry/cellprofiler/resultson the host to any machine with a windows manager (Mac, Windows, Ubuntu Desktop, etc.) at a path equivalent to the path used in the container (i.e. create/lab/dataroot directory and place everything under it). For example:mac> rsync -rP myhost:/data/disk1/20180101_codex_spleen/20180101_codex_mouse_spleen_balbc_slide1/output/v00/cytometry/cellprofiler/* /lab/data/20180101_codex_spleen/20180101_codex_mouse_spleen_balbc_slide1/output/v00/cytometry/cellprofiler/ - Create a network drive (e.g. w/ samba on Mac) shared with the host running docker and symlink a
/lab/datadirectory to it. For example on a Mac, if the samba mount is at/Volumes/disk1then the data could linked withmac> mkdir /lab; cd /lab; ln -s /Volumes/disk1/ /lab/data
After copying or linking the data, CPA can be pointed at the CPA_Exp_Cell.properties properties file and run as usual.