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Software package for https://doi.org/10.1016/j.celrep.2021.110000
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jkfindeisen/nucleoid_detection_and_kinetics_2021
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Software demonstration set for "The TFAM to mtDNA ratio defines inner-cellular nucleoid populations with distinct activity levels" https://doi.org/10.1016/j.celrep.2021.110000 by Christian Brüser, Jan Keller-Findeisen, and Stefan Jakobs Department of NanoBiophotonics, Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Biophysical Chemistry; Clinic of Neurology, High Resolution Microscopy of the Cell, University Medical Center Göttingen; Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy Göttingen, Germany Software description ==================== The software is written in Matlab and tested on Matlab 2020. example_colocalize_DNA_EdU_spots.m - combines estimated DNA and EdU spots to determine the fraction of EdU active spots example_detect_nucleoids.m - identifies DNA and EdU spots in STED images example_detect_nucleus.m - identifies the nucleus of STED images fit_timeseries_edu_positive_nucleoids.m - fits the determined fraction of EdU containing spots with suitable model functions folder code - additional software folder data - example data Usage instructions and example data set ======================================= Please run the example_xxx.m scripts to see exemplary steps of the analysis procedure focused on a dataset of a HDFa cell incubated with EdU for 18 hours and measured for mitochonrdrial DNA as well as EdU in STED mode. Please run script fit_timeseries_edu_positive_nucleoids.m to reproduce values given in Supplementary Table 1 and Fig. 1f in the manuscript. Run initialize.m once to add all relevant folders to the Matlab path. License ======= The code is MIT licensed (see LICENSE.txt)
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Software package for https://doi.org/10.1016/j.celrep.2021.110000
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