Gating

Gating is an extension for 'minerva_analysis' that enables filtering of selected image channels based on the channel's intensity value range. Users can visualize the subset of segmented cells that are selected based on the channel filters and export the list to a csv file.

Installation

For End Users

Download latest release and execute it. This will start a local server on your machine. Open the browser and navigate to: http://mts-lsp-l06208:8000/

For Developers

1. Clone locally from Github: git clone -b gating git@github.com:labsyspharm/minerva_analysis.git
   • or, switch to branch: git switch gating
2. Run from readme.md (no new env updates)

Functionality

Channel Viewer

Select channels for viewing under 'Channels' and use the slider to adjust contrast. Click on 'auto' for auto-contrasting using a Gaussian Mixture Model with 3 components (displayed above the slider with the pixel-level distribution).

Channel Gating

Select channels for gating under 'CSV Gating' and use the slider to filter segmented cells by intensity range. Click on 'auto' for auto-gating using a Gaussian Mixture Model with 2 components (displayed above the slider with the cell-level distribution).

Viewing channels for DNA1 (blue) and CD7 (red). Gating for cells with high intensity in CD7 channel.

Multiple Channels

Up to 3 channels can be used for gating segmented cells. Click 'Centroids (OR-mode)' to visualize the cells that are selected for each channel gate.

Viewing and gating DNA1 (blue) and CD7 (red) channels. Centroids indicate selected cells for each channel.

Download Gating Info

Download a CSV file with the selected channel gates and their respective ranges and a CSV file with the gated selections of segmented cells.