lexxx233 / cytobrowser

CytoBrowser, a JavaScript and Node.js driven environment for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images.

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}
}

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. ↩