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Example data

Four (4) human tissue cores 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 EMIT (Exemplar Microscopy Images of Tissues) TMA22 (Synapse ID: syn22345750). The tissues cores 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 using the following commands:

Step 1: Download

# Activate the CyLinter virtual environment.
conda activate cylinter

# Install the Synapse client.
conda install -c bioconda synapseclient

# Mac/Linux users, run the following command to download the demo dataset:
synapse get -r syn52859560 --downloadLocation ~/Desktop/cylinter_demo  # Enter Synapse ID and password when prompted.

# PC users, run the following command to download the demo dataset:  
synapse get -r syn52859560 --downloadLocation C:\Users\<username>\Desktop\cylinter_demo --multiThreaded  # Enter Synapse ID and password when prompted.
  • The demo dataset can also be downloaded directly from the Sage Synapse website here: syn52859560.

Step 2: Configure

After downloading the exemplar dataset, open the YAML configuration file and update the inDir and outDir parameters with user-specific directory paths. All other settings are pre-configured for use with the demo dataset.

inDir: /Users/<username>/Desktop/cylinter_demo
outDir: /Users/<username>/Desktop/cylinter_demo/output
.
.
.

Step 3: Run

To run Cylinter on the demo dataset, pass the YAML configuration file to the cylinter command:

# for Mac:
cylinter --module <module-name>(optional) ~/Desktop/cylinter_demo/cylinter_config.yml  

# for PC:
cylinter --module <module-name>(optional) C:\Users\<username>\Desktop\cylinter_demo\cylinter_config.yml