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openRNA

Open-source toolbox and workflows for automated analysis of RNAscope data from human and mouse

Current Features

1. Automated analysis of RNAscope data

  • Automated cell counting and segmentation (currently works for TIF and CZI files only)

  • Mouse and Human workflows

    • Same matlab toolbox is used for both data sets.

2. Image-level and ROI-level (or nuclei-level) statistics

  • Outputs 2 CSVs after automated analysis of TIF or CZI file(s)

    • man.csv represents image-level summary statistics for each channel of input data

    • longdat.csv represents ROI-level (or nuclei-level) summary statistics for each channel of input data

  • These two CSVs can be read into R (or python, or Matlab, or your favorite statistical sofware tool).

Example: Automated Cell Counting and Segmentation

The input czi file has the following channels:


The corresponding segmentions from Dotdotdot:


Under Construction

  • Data visualization of Image-level and ROI-level statistics
  • Implementation of automated analysis of LIF (z-stack) files
  • Python version of toolbox

Forked from LieberInstitute/dotdotdot