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Example data

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 ( Once registered, the example dataset can be downloaded with the following commands:

# Activate the CyLinter virtual environment.
source ~/cylinter/bin/activate

# 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

After downloading, open the YAML configuration file in ~/Desktop/cylinter_demo/config.yml and update the in_dir and out_dir parameters with user-specific directory paths. All other settings are pre-configured for use with the exemplar dataset.

in_dir: /Users/<username>/Desktop/cylinter_demo
out_dir: /Users/<username>/Desktop/cylinter_demo/output

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