Wei Ouyang oeway

I am working with Deep Learning based image analysis and modeling, excited about biology, deep neural nets, open source, Python and JavaScript.

oeway / ImageJ.JS-slides-for-OME-Meetings-2021.md

Last active May 25, 2021 19:25

ImageJ.JS: ImageJ in the browser

Wei OUYANG

Emma Lundberg Group @ KTH Royal Institute of Technology

oeway / HPACellAtlasImages.imjoy.html

Last active May 23, 2021 22:44

	<docs>
	# HPA Cell Atlas Images

	This plugin uses the virtual stack api of ImageJ.JS to display all the HPA Cell Atlas images (v18).
	</docs>

	<config lang="json">
	{
	"name": "HPACellAtlasImages",
	"type": "iframe",

oeway / imjoy-app-engine-demo.ipynb

Created May 20, 2021 12:55

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oeway / broadcastConnectionOnly.js

Last active May 16, 2021 14:06

Connecting to another ImJoy plugin in the same browser via broadcast channel and webRTC (only works with Chrome and FireFox)

	/**
	* Contains the routines loaded by the plugin iframe under web-browser
	* in case when worker failed to initialize
	*
	* Initializes the web environment version of the platform-dependent
	* connection object for the plugin site
	*/
	import { connectRPC } from "./pluginCore.js";
	import { RPC, API_VERSION } from "./rpc.js";
	import { MessageEmitter, randId, normalizeConfig } from "./utils.js";

oeway / cross-tab-webrtc.html

Created May 15, 2021 15:08

	<body>
	<button id="button" onclick="connect()">Connect</button>
	<div id="div"></div><input id="chat"></input><br>
	<script src="https://webrtc.github.io/adapter/adapter-latest.js"></script>
	<script>
	var pc = new RTCPeerConnection(), dc, enterPressed = e => e.keyCode == 13;

	var connect = () => init(dc = pc.createDataChannel("chat"));
	pc.ondatachannel = e => init(dc = e.channel);

oeway / HPA-UMAP-Nucleolus.imjoy.html

Created May 14, 2021 19:39

	<docs>
	[TODO: write documentation for this plugin.]
	</docs>

	<config lang="json">
	{
	"name": "HPA-UMAP-Nucleolus",
	"type": "web-worker",
	"tags": [],
	"ui": "",

oeway / imjoy-slides-plotly.md

Last active May 14, 2021 15:24

oeway / NGFF-Loader.imjoy.html

Last active May 18, 2021 18:57

	<docs>
	# NGFF image file Loader for ImageJ.JS

	[Next-generation file formats](https://ngff.openmicroscopy.org/latest/) is a specification for storing bioimaging data in the cloud.

	This plugin enalbes loading NGFF image into ImageJ.JS.

	The implementation is adapted from the [OMERO ImJoy](https://github.com/will-moore/omero-imjoy) made by @will-moore

	</docs>

oeway / HPA-UMAP-Studio.imjoy.html

Last active May 14, 2021 17:30

	<docs>
	[TODO: write documentation for this plugin.]
	</docs>

	<config lang="json">
	{
	"name": "HPA-UMAP-Studio",
	"type": "web-worker",
	"tags": [],
	"ui": "",

oeway / uniprot_to_emsembl_conversion.py

Created May 4, 2021 21:16

	import gzip

	# download idmapping.dat.gz from uniprot
	# wget ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz
	id_mapping_file = './idmapping.dat.gz'

	id_mapping = {}
	for line in gzip.open(id_mapping_file):
	line = line.decode('utf8').strip()
	ac, pred, obj = line.split('\t')