Encounter of SMCs with a Roadblock

We are pleased to announce that we are making this repository publicly available. It provides insight into DNA loop extrusion and the interaction between SMC complexes and a roadblock.

LEADS 0.1.0

First release.

We are happy to release the first working LEADS program for the analysis of stretched DNA in fluorescence microscopy.

LEADS can be used for both analysis and fast visualization of the image frames.

Features of kymograph_gui

• Multicolor visualization.
• Kymograph of selected ROIs. Realtime update of the kymograph.
• Kymograph analysis.
• Peak finding from the kymograph.
• Recognizing different peaks and making a distinction among them.
• Colocalizing peaks from different colors.
• Kinetics of changes in DNA. e.g. DNA Loop extrusion rates
• MSD calculation of peaks.
• Saving high-quality videos
• Saving analyzed data in hdf5 format
• Saving and loading parameters. Allows continuing analysis where you left the last time.

Features of crop_images_gui

• Loading and visualization of a large dataset
• Multicolor splitting of sequential (alternative) images. Any number of colors.
• Background substraction.
• Chromatic shift correction.
• Cropping multiple ROIs at the same time.
• Loading and saving roi files from imageJ.

Authors contributed to this release (Alphabetical)

• Biswajit Pradhan
• Roman Barth