Microscopy tree selector

This repository contains the codes for the interactive microscopy image type selector tree with available nucleus segmentation methods listed.

Prerequisites

To use this tool you need to:

• Install Node.js

Installation

1. Clone this repository with

	git clone https://github.com/spreka/microscopy-tree.git

2. Run

npm install
npm run build
npm start

Usage

Structure

Initially, the full tree is displayed on the left with all nodes visible, and the info panel on the right shows details about the currently selected node (root initially):

• name of the selected node corresponding to image type
• a couple of sample images of the given type
• (a table showing information about the selected sample image when clicked, otherwise hidden)
• applicable methods in a table

How to interact with the tree

• Clicking on a node will select it, hide the irrelevant parts of the tree and increase icon sizes for better visibilty. The info panel on the right will update its data accordingly.
• Clicking on a node higher in the tree than the currently selected one will open existing paths.
• Clicking on a sample image in the info panel will reveal a table under the images with data of the selected sample image whose border is turned to blue.
• Both tables will have clickable links to data and code sources (in progress).

Data structure

The data is currently stored in json.js, a simple text file in json format. Methods are stored in a separate data file seg_methods.js.

Deployment

The tree is deployed on Github pages.

Contribution

Methods and datasets are welcome to be added to the tree. For more information, please contact us at [email protected].

Citation

Please cite our bioRxiv paper if you use the tree (coming soon).