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 fork[^1] of TissUUmaps aimed at Cytology
[^1]: TissUUmaps originally had a strict "clientside only" policy, which was incompatible with the CytoBrowser collaborative aim.
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

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You can try out a limited bandwidth live demo of the latest stable release (just running npx cytobrowser) here.

#### Express setup
1. Install Node.js
2. Run npx cytobrowser --open-browser[^2]
[^2]: If (on Windows) you get ENOENT: no such file or directory..., the try running npm install -g npm

Done! 😊

You may now populate your ./data directory, see below for further info.
 

#### Slightly longer example, cloning the latest sources from GitHub (instead of using npx)

#Clone from github
git clone https://github.com/MIDA-group/CytoBrowser.git
cd CytoBrowser
#Install the necessary dependencies
npm install
#Optionally switch to develop version git switch develop

#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

#More generally, to start the web server on a specified port
node cytobrowser.js [hostname] [port]

node cytobrowser.js --help
  
#Optionally open an ssh-pipe from your local machine to the web server
ssh -L 8080:localhost:8080 remote.host  
#Enjoy! =)

Some additional info can also be found in the INSTALL.md file.

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Current list of branches:
* stable - Main stable branch, official releases are from this branch;
* develop - Main development branch, less stable but more up-to-date - most often a good choice;
* devel/multi-image - Work in progress to support multiple layers of images (for correlative multimodal analysis);
* devel/multi-image-autoload-hack - Small add-on to hide images with suffix '_FL', and autoload them together with corresponding non-hidden images with same prefix.

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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 that you experience.

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We are very happy for contributions to further improve CytoBrowser, take a look at CONTRIBUTING.md to get started.

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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}
}
``

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This work is supported by: VINNOVA grants 2017-02447, 2020-03611 and 2021-01420, and Swedish Research Council proj. 2017-04385.