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 (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 cellmask (e.g., 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 inDir and 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