Part of our commitment to open science comes in the form of open source software. Over the years, we have produced tools for image analysis and other relevant tasks. Our central CMCB GitHub site collects these software projects.

  1. KiT
  2. SiD
  3. MT-directionality
  4. PERSIST
  5. CellMigration
  6. VolumeFinder
  7. Tip Tracker Positioning

comets KiT (Kinetochore Tracking) is a MATLAB program for tracking kinetochores in 2D or 3D, and in multiple channels that evolved from earlier software for particle tracking (u-Track; Jaqaman et al., 2008), kinetochore tracking (MaKi; Jaqaman et al., 2010) and kinetochore track analysis (CupL; Vladimirou et al., 2013) and incorporates numerous enhancements and major new features. Movies are loaded through the Bioformats package (Linkert et al., 2010), which is automatically downloaded, enabling compatibility with a vast range of microscopy data formats.


KiT 1.5.06 - see: Armond et al, Bioinformatics. 2016 Jun 15;32(12):1917-9. PMID: 27153705

KiT 2.1.11 - see: Olziersky et al, Methods Cell Biol. 2018;145:1-27. PMID: 29957199. This version now includes a user friendly GUI


No installation is necessary, simply copy the source code to the directory of your choice. Enter that directory within MATLAB (use directory toolbar at top, or 'cd' command) and then enter commands.


Download the source code from our GitHub page.

luttonSID (Spot Intensity Detector) is a MATLAB program for detecting spot intensities in microscopy images in 2D or 3D, in up to four channels.


No installation is necessary, simply copy the source code to the directory of your choice. Enter that directory within MATLAB (use directory toolbar at top, or 'cd' command) and then enter commands.


Download the source code from our GitHub page.

MTdirectionality MT-directionality is a MATLAB script to determine microtubule growth orientation. It uses PlusTipTracker output to determine microtubule growth orientation relative to a user-specified axis of the cell. The script will plot a map of tracks overlaid onto an image of the cell colour-coded for their directionality. It will also generate a histogram with the relative frequency of angles and determine the Kuiper statistics relative to a random distribution. For examples please see Theisen et al. Dev Cell 2012 and Mogessie et al., eLife 2015.


Download the source code from our GitHub page.

curvature PERSIST allows fast calculation of different measures for the directional persistence of cell migration from tracking data of XY positions over time. This package contains 2 programme files and 2 test datasets that have been used in the original publication (Theisen et al. (2012) Developmental Cell 23:1153-1166).


The programs can be compiled and run on Mac (requires Xcode to be installed) and Linux from the Terminal without any additional software.


Download the source code from our GitHub page.

cellmigration CellMigration is a set of functions to load particle tracks and analyse 2D cell migration in Igor Pro.


Download the source code from our GitHub page.



volfinder VolumeFinder is a set of procedures for volume analysis and spatial statistics of 3D point sets in IgorPro. A detailed walkthrough of the analysis procedure is available bundled with the source code.


Download the source code from our GitHub page.




Spatial positioning of tip trackers
SpatialPositioning

Here we provide MATLAB scripts for the analysis of the relative spatial positioning of EB comets in cells and in vitro as used for Roth et al., J Cell Science 2018.

LineScans.m is used to superaverage multi-colour linescan data as can be obtained from fixed cell imaging stained with different antibodies for tip tracker proteins - in our case EB1, EB2 and EB3. Data from different cells and experiments are averaged by using the half-maximal intensity of both EB1 and EB3 peak as reference. The data are provided as textfile outputs from the ImageJ "Plot Profile" function.

PairedNucleotides.m is used to simulate the distribution of GTP, GDP/Pi and GDP as a function of distance from the microtubule end and calculate the distribution of pairs of nucleotides. The script outputs an eps file with plots for three different parameter settings, which can easily be modified in the source code.

DualColourKymograph_Analysis.zip contains a group of functions to superaverage intensity distributions from dual colour experiments with sequential imaging. The input are kymographs of the red and green channel movies. In the first step, continuous growth phases are selected using the MATLAB-ImageJ interface in the red channel. Then, the temporal shift is corrected and averaged intensity data obtained for each growth phase before superaveraging data and calculating peak difference distributions.

These are Matlab functions that have been tested to run on MATLAB_R2012b. Please see description in the MATLAB function itself and the original publications for more detail: Roth et al. (2018) Journal Cell Science.



Download the source code from our GitHub page.