Downloads

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

The zip file "2016-05-20_supplementarydata.zip" contains the source code of the image analysis pipeline. The package was developed in Mathematica V10.2 (Wolfram Research, Inc.). A user interface has been developed that allows to setup the parameters for cell nuclei segmentation, alpha shape computation and cell graph generation.

  • CellNucleiSegmentation_v8.m is a Mathematica package file containing the source code of the cell nuclei segmentation pipeline and the user interface.
  • CellNucleiSegmentationGUI.nb is a Mathematica notebook file containing the user interface and a short readme how to use it.

The zip file "2016-11-10_exampledatasets.zip" contains two exemplary raw image stacks (dataset S9 and M2) in TIF format.

 Feel free to contact us if you find any bugs or if you have suggestions to improve the image analysis pipeline.

File Size Upload date
Package icon 2016-05-20_supplementarydata.zip 1.04 MB 20/05/2016
Package icon 2016-11-10_2016-11-10_exampledatasets.zip 891.85 MB 10/11/2016
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition

Source code of the Lines-of-Sight decomposition algorithm. Fell free to download it and use it. Please notify us if you use it for your own purposes. Do not hesitate to contact us if you find mistakes or have suggestions for improvement. The code was developed and tested with Mathematica version 9. The zip folder contains three Mathematica files. The .cdf file can be viewed with the free Wolfram CDF-Player (download from http://www.wolfram.com/cdf-player/ (link is external)).

 

To find more details, please see:


Mathew B, Schmitz A, Muñoz-Descalzo S, Ansari N, Pampaloni F, Stelzer EHK, Fischer SC (2015), Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition. BMC Bioinformatics 16:187

File Size Upload date
Package icon 2015-06-12_los_sourcecode.zip 166.44 MB 12/06/2015
Introductions to Light Sheet-based Fluorescence Microscopy (LSFM, SPIM, DSLM)

The technology behind light sheet-based fluorescence microscopy and its various implementations (SPIM, single/selective plane illumination microscopy; DSLM, digital scanned laser light fluorescence light microscopy) are explained in various different texts, presentations and figure collections. You are welcom to download and use the resources. Please inform us, if you use the material. Please do not hesitate to inform us about any mistakes of any kind.

File Size Upload date
PDF icon PDF (6MB) LSFM PowerPoint Presentation 5.97 MB 31/01/2013
File LSFM PowerPoint Presentation (335MB) 334.45 MB 31/01/2013
PDF icon mDSLM Poster (2 MB) 1.81 MB 21/10/2014
Introduction to Mathematica

Material of the last one week course Introduction to Mathematica in March 2017. Fell free to download it and use it. Please notify us if you use it for your own courses. Do not hesitate to contact us if you find mistakes or have suggestions for improvement. When opening the folder first run IntroductionMathematicaMaster.nb by opening the file in Mathematica and click on the time table. The buttons will then give you access to the different sections of the course. Mac users will have to replace "\\" in the file paths with "//". Note that to evaluate the Master notebook the suggestion bar has to be switched off. To switch it off go to Edit/Preferences/Interface and untick the third last box "Show Suggestion Bar after last output".

File Size Upload date
Package icon 2017-05-19_introductionmathematicamarch2017.zip 65.98 MB 19/05/2017
Two- and three-dimensional image processing with Mathematica

Material of the last one day course Two- and three-dimensional image processing with Mathematica in September 2015. Fell free to download it and use it. Please notify us if you use it for your own courses. Do not hesitate to contact us if you find mistakes or have suggestions for improvement. When opening the folder first run ImageProcessingMaster.nb by opening the file in Mathematica and choosing Evaluation/Evaluate notebook. The buttons will then give you access to the different sections of the course. Mac users will have to replace "\\" in the file paths with "//". Note that to evaluate the Master notebook the suggestion bar has to be switched off. To switch it off go to Edit/Preferences/Interface and untick the third last box "Show Suggestion Bar after last output".

File Size Upload date
Package icon 2015-10-20_imageprocessing2015.zip 82.86 MB 20/10/2015
Statistical data analysis with Mathematica

Material of the last one day course Statistical data analysis with Mathematica in September 2015. Fell free to download it and use it. Please notify us if you use it for your own courses. Do not hesitate to contact us if you find mistakes or have suggestions for improvement. When opening the folder first run DataAnalysisMaster.nb by opening the file in Mathematica and choosing Evaluation/Evaluate notebook. The buttons will then give you access to the different sections of the course. Mac users will have to replace "\\" in the file paths with "//". Note that to evaluate the Master notebook the suggestion bar has to be switched off. To switch it off go to Edit/Preferences/Interface and untick the third last box "Show Suggestion Bar after last output".

File Size Upload date
Package icon 2015-10-20_statisticaldataanalysis2015.zip 18.62 MB 20/10/2015