CytoBrowser

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

1. Handling z-stacks (focus stacks), ctrl-scroll on your mouse to focus
2. Multi-user shared view with follow options, also when changing images and annotation layers
3. URL encodes the current view and annotation layer; easy to bookmark views, copy and share
4. Point and region annotations with class label and textual comments
5. Automatic server side storage of annotations; import/export of annotations in JSON format

Example

#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! =)

Citing

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}
}

Issues

We aim to support all modern browsers. Since development mostly utilizes the Chrome browser, that one can be expected to give the least troublesome usage experience. Please don't be shy to report issues you experience.

Acknowledgement

This work is supported by: VINNOVA grants 2017-02447 and 2020-03611.

Footnotes

1. TissUUmaps originally had a strict "clientside only" policy, which was incompatible with the CytoBrowser collaborative aim. ↩