.. BacStalk documentation master file, created by sphinx-quickstart on Sat Mar 17 12:03:46 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to the BacStalk documentation! ====================================== :program:`BacStalk` is an interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species (e.g. *Escherichia coli*, *Bacillus subtilis*, *Pseudomonas aeruginosa*, etc.) and stalk-forming bacteria (e.g. *Caulobacter crescentus*, *Hyphomonas neptunium*, *Brevundimonas aveniformis*, etc.). BacStalk uses phase contrast, brightfield, and/or fluorescence images to segment bacteria and generate demographs, kymographs, histograms, scatterplots. For stalked bacteria, BacStalk can also identify *hardly-visible* bacterial stalks to observe *stalk formation dynamics* and *bud cell growth*. Fluorescence images can be used to measure protein expression patterns along cells and stalks. .. image:: images/example.png :alt: Example image from BacStalk :width: 100 % :align: center BacStalk uses a very intuitive and modern graphical user interface (GUI, see :ref:`Screenshots`) and provides all tools required for file-handling, metadata extraction, cell/stalk/bud segmentation, cell tracking, data analysis and visualization. BacStalk generates publication-grade figures with only a few clicks. Although BacStalk is based on the Matlab-software, it does not require any programming knowledge to use. Getting started ############### .. toctree:: :maxdepth: 2 usage/installation usage/fileInput usage/segmentation usage/analysis Video tutorials ############### .. toctree:: :maxdepth: 1 usage/video_tutorials More information ################ .. toctree:: :maxdepth: 2 usage/screenshots usage/tools Contact us! ########### BacStalk was developed by Raimo Hartmann and Muriel van Teeseling at the `Max Planck Institute for Terrestrial Microbiology `_ and `Phillips-Universität `_ in Marburg in the labs of `Knut Drescher `_ and `Martin Thanbichler `_. You can reach us at `bacstalk@gmail.com `_. How to cite ########### Please use the following reference for citing this software after you have used it: - Hartmann, R., van Teeseling, M. C. F., Thanbichler, M. & Drescher, K. BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology. *Molecular Microbiology* (**2020**). `doi:10.1111/mmi.14501 `_ Credits ####### We would like to acknowledge the authors of the following Matlab File Exchange contributions: - David Sampson and Ben Tordoff `GUI Layout Toolbox `_ - Ben Tordoff `Splash Screen `_ - Manuel Guizar `Efficient subpixel image registration by cross-correlation `_ - Reza Ahmadzadeh `isToolboxAvailable `_ - Ronald Ouwerkerk `Neighbour points in a matrix `_ - Daniel Terry `parfor_progressbar `_ - Adam Auton `Red Blue Colormap `_ - Yair Altman `Enable/disable entire figure window `_ & `findjobj `_ and - John C. Crocker and David G. Grier `Band-pass filter `_