Introduction#

A pyHiM output example

In the context of structural biochemistry, pyHiM software provides tools to process multiplexed DNA-FISH data produced by Hi-M experiments as well as visualization tools to explore the results.

Note

For more information on Hi-M, please see the following resources:

Concept#

This software calculates the 3D positions of a set of DNA-loci, referred to as barcodes.

Data acquisition is performed sequentially, in a series of cycles combining the acquisition of a single barcode with a fiducial marker common to all cycles and later used for drift correction.

Each set of barcode coordinates will be associated with its corresponding cell by using masks (segmented nuclei stained with DAPI for instance).

At the end of the analysis, pyHiM will output several files describing the composition (barcodes), localization and 3D-coordinates of all individual traces detected.

Note

Optionally, pyHiM also provides a basic tool to detect single RNA types but does not support processing of multiple RNA species or proteins-FISH data.

Type of data#

For a given region of interest (ROI), a minimal Hi-M set of data contains:

  • Images of nuclei

  • Images of DNA-FISH barcodes acquired during successive hybridization cycles

  • Fiducial images for both nuclei and barcodes.