Bioengine web client

Standalone web client for run models on Bioengine. Directly run the advanced deep-learning models in the bioimage.io model zoo 🦒!

Online demo: https://bioimage-io.github.io/bioengine-web-client/

Functionality:

• Using ImageJ.js as a viewer and preprocessor.
• Loading and displaying sample input and output images for a specific model.
• Submitting images to Bioengine and displaying results.
• Image tiler allows to run model on large images.
• Export ImJoy API for using as a plugin in ImJoy.
• Integrated with Bioimage.IO chatbot

ImJoy API

This web client supports two-way integration with ImJoy, meaning you can either use it as an ImJoy plugin or load other ImJoy plugins into it.

The following ImJoy API is supported:

API	Description	Parameters
runModel	Run model on current image(in the viewer)
setParameters	Set model parameters	parameters: object
listModels	List all models, return an array of model rdf objects
setModel	Set the current model, support input a model_id or model name or nick name	model: object, string
setTiling	Set the tile and overlap size for large images	tileSizes: object; tileOverlaps: object
waitForReady	Wait for the model to be ready
setServersetting	Set the server url, and service id,	serverUrl: string; serviceId: string

Usage example:

const client = await api.getWindow("bioengine-web-client");
await client.waitForReady();
console.log(await client.listModels());
// load cellpose model and run it
await client.setModel("Cellpose");
await client.setParameters({ diameter: 30, model_type: "cyto" });
await client.setTiling({ x: 64, y: 64 });
await client.runModel();

url parameters

• model: model name or model id
• server_url: the bioengine server url
• triton_service_id: the triton service id

Example: Click here

As an Bioimage.IO chatbot extension

This web client can be used as an extension of the Bioimage.IO chatbot to run models on Bioengine. You can load this url in the chatbot to use it as an extension:

https://bioimage-io.github.io/bioengine-web-client/chatbot-extension.imjoy.html

Development

$ npm install -g pnpm  # install pnpm globally
$ pnpm install         # install dependencies
$ pnpm run dev         # serve with hot reload