CytoBrowser, a JavaScript and Node.js driven environment for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images.
Origintating as a fork1 of TissUUmaps aimed at Cytology
- Handling z-stacks (focus stacks), ctrl-scroll on your mouse to focus
- Multi-user shared view with follow options, also when changing images and annotation layers
- URL encodes the current view and annotation layer; easy to bookmark views, copy and share
- Point and region annotations with class label and textual comments
- Automatic server side storage of annotations; import/export of annotations in JSON format
#Clone from github git clone https://github.com/MIDA-group/CytoBrowser.git cd CytoBrowser #Install the necessary dependencies npm install #Put your OpenSeadragon compatible images in the 'data/' directory #For converters, see e.g.: http://openseadragon.github.io/examples/creating-zooming-images/ #Or download an example image and convert it to Deep Zoom Image (dzi) format #(There are more examples in the 'examples/' directory) ./examples/Zeiss-1-Stacked.sh #This requires bftools and libvips #Start the web server on a free port on localhost, and open a browser node cytobrowser.js --open-browser #Optionally open an ssh-pipe from your local machine to the web server ssh -L 8080:localhost:8080 remote.host #More generally, to start the web server on a specified port node cytobrowser.js [hostname] [port] #Enjoy! =)
If you find the CytoBrowser software useful in your research, please consider citing the following article:
Rydell C and Lindblad J. "CytoBrowser: a browser-based collaborative annotation platform for whole slide images". F1000Research 2021, 10:226 (https://doi.org/10.12688/f1000research.51916.1)
@article{ 10.12688/f1000research.51916.1,
author = {Rydell, C and Lindblad, J},
title = {CytoBrowser: a browser-based collaborative annotation platform for whole slide images [version 1; peer review: awaiting peer review]},
journal = {F1000Research},
volune = {10},
year = {2021},
number = {226},
doi = {10.12688/f1000research.51916.1}
}
This work is supported by: VINNOVA grants 2017-02447 and 2020-03611.
Footnotes
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TissUUmaps originally had a strict "clientside only" policy, which was incompatible with the CytoBrowser collaborative aim. โฉ