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Simple segementation and analysis of spatial data using CellProfiler and Spectre


1. Cell segmentation

Simple segmentation using nuclear expansion with CellProfiler

This is the simplest form of cellular segmentation. The nuclear signal is identified, and the boundary is expanded outwards by a certain number of pixels. This then becomes the boundary of the cell mask. Although a very simplistic approach, only nuclear signal is required.

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2. Spatial analysis

Simple spatial analysis with Spectre

A simple analysis workflow in R using Spectre, with simple cell masks.

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FCS conversion and analysis in FlowJo

An analysis protocol to facilitate the creation of FCS files from IMC data and subsequent analysis using FlowJo.

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