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Wei Ouyang oeway

  • Science For Life Laboratory
  • Stockholm
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oeway / README.md
Created June 30, 2024 21:25
Python script for setting up a WebSocket proxy in Google Colab to communicate between the embedded web page with a WebSocket server.

Description for colab_websocket.js

Title: colab_websocket.js

Description: This JavaScript file implements a WebSocket client for Google Colab that facilitates communication between the Colab notebook and a WebSocket server. It includes buffer handling for binary data and a simple debug console for sending and receiving messages.

Description for colab_websocket_proxy.py

Title: colab_websocket_proxy.py

import sys, os
import imagej
import scyjava as sj
import argparse
import asyncio
import traceback
import numpy as np
import xarray as xr
from jpype import JOverride, JImplements
from imjoy_rpc.hypha import connect_to_server
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "CodeInterpreter",
"type": "window",
"tags": [],
"ui": "",
<docs>
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "ImageViewerServices",
"type": "web-worker",
"tags": [],
"ui": "",
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@oeway
oeway / README.md
Last active October 11, 2023 16:43

SAM for the BioEngine

Inference

Here are some files for converting SAM models to make it available in the BioEngine (local deployment: https://github.com/oeway/bioengine/).

The tree strcture for the model repository is like this:

├── sam-backbone
│ ├── 1
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "React UI Plugin",
"type": "window",
"tags": [],
"ui": "",
<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>
<config lang="json">
{
"name": "stlite Demo",
"type": "window",
"tags": [],
"ui": "",
import asyncio
import threading
from concurrent.futures import ThreadPoolExecutor
from imjoy_rpc.hypha import connect_to_server
import time
class BackgroundServer:
def __init__(self, server_url):
self.loop = None
# pip install imjoy-rpc numpy qrcode[pil]
# Code adopted from https://github.com/Khalil-Youssefi/qrcodeT/tree/master
# Released under MIT license
import qrcode
import numpy as np
def qrcode2text(img):
bindata = np.array(img)[::10,::10] + 0
if bindata.shape[0] % 2 != 0: