Four human tissue samples are provided as CyLinter demonstration data: normal kidney cortex, mesothelioma, glioblastoma, and normal tonsil. These imaging data were collected by CyCIF and are derived from a tissue microarray collected at the Laboratory of Systems Pharmacology referred to as Exemplar Microscopy Images of Tissues (EMIT TMA-22, Synapse ID: syn22345750). The tissues were imaged at 20X magnification using a 0.75 NA objective and 2x2-pixel binning.
Access to the demonstration dataset requires free registration at the Sage Synapse data repository (https://www.synapse.org/). Once registered, the example dataset can be downloaded with the following commands:
Step 1: Download
# Activate the CyLinter virtual environment. mamba activate cylinter # Install Synapse client. mamba install -c bioconda synapseclient # Mac users can download the demo dataset using the 'prep' command. prep cylinter_demo ~/Desktop/cylinter_demo # Enter Synapse ID and password when prompted. # PC users, run the following command to download the demo dataset: synapse get -r syn25685780 --downloadLocation C:\Users\<username>\Desktop\cylinter_demo --multiThreaded
PC users: note that the downloaded CSV file names will be in all lowercase. These must be re-formatted to match the way they are specified in the template configuration file (
config.yml) by capitalizing the ‘m’ in
unmicst-1_cellMask) for all four files.
Step 2: Configure
After downloading the exemplar dataset, open the YAML configuration file in
~/Desktop/cylinter_demo/config.yml and update the
outDir parameters with user-specific directory paths. All other settings are pre-configured for use with the exemplar dataset.
inDir: /Users/<username>/Desktop/cylinter_demo outDir: /Users/<username>/Desktop/cylinter_demo/output . . .
Step 3: Run
Pass the configuration file to the
cylinter command to run Cylinter on the example data:
# for Mac: cylinter --module <module-name>(optional) ~/Desktop/cylinter_demo/config.yml # for PC: cylinter --module <module-name>(optional) C:\Users\<username>\Desktop\cylinter_demo\config.yml