MINA Analyst

This page includes resources published in our paper titled “Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue” (Nature Protocols, 2021, https://doi.org/10.1038/s41596-021-00518-0).

Right click each link and use “Save link as” to download the following files as needed:

MinaAnalyst software package (current version)

Example MINA data – The example data set has a size of 120 GB, and contains 2 fields of view (FOVs).

Default MINA image file naming conventions (used in the example data set and recognized by MinaAnalyst)

Frequently asked questions and answers
Q: Running MinaAnalyst with the example MINA data generates error. How to solve the issue?
A: Please note the example MINA dataset has two fields of view. So in the MinaAnalyst window, the “Total number of fields of view” should be 2. In addition, please remove all spaces in the file path (folder names) where the example MINA data is downloaded, or replace them with underlines. Please check if the input “Experimental file path” text ends with a “\” or “/” as in the default entry, which is needed for MinaAnalyst to run correctly.

Q: MATLAB shows error messages stating certain functions are not defined. How to solve the issue?
A: MinaAnalyst requires the Curve Fitting Toolbox and the Image Processing Toolbox of MATLAB to be installed. Please check if these Toolboxes have been installed during MATLAB installation.

Q: Can I directly run MinaAnalyst or use the example MINA data in the downloaded zip folder?
A: No. Please first unzip both.