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