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import argparse
import json
import sys
from omero.gateway import BlitzGateway
from omero.cli import cli_login
from omero.model import StatsInfoI
from omero.rtypes import rdouble
# Requirements:
# hdf5>=1.10.5
# h5py>=3.0
# conda install -c conda-forge hdf5 h5py
import logging
from urllib.parse import urlparse, urlunparse
import numpy as np
import h5py
import zarr
@mikrkilk
mikrkilk / omero_figure_channel_names.js
Last active April 18, 2022 17:39
Omero utility scripts
javascript:(function(){
let infotab = document.getElementById('infoTab').children[0].children[2];
let channels = infotab.children[0].children[1].children[0].lastElementChild.textContent.trim().split(', ');
let channelsliders = document.getElementById('channel_sliders').children[0];
for(i=0;i<channels.length;i++) {
let p = document.createTextNode(channels[i]);
let br = document.createElement('br');
channelsliders.children[i].insertBefore(br,channelsliders.children[i].firstChild);
channelsliders.children[i].insertBefore(p,channelsliders.children[i].firstChild);
}

Exemplar - run ASHLAR on demo data with the batch script

  1. Download and unzip FIJI, move the FiJji.app folder to C:\Users\Public\Downloads\

  2. Install BaSiC by following the instructions under the Install via the Fiji Updater section on this page

  3. Save the imagej_basic_ashlar.py to C:\Users\Public\Downloads\Fiji.app\plugins\

  4. Launch command prompt

@mikerourke
mikerourke / install-yarn.md
Last active June 3, 2022 12:41
Upgrades/Installation in Cloud9

Installing Yarn in Cloud9

You can't just follow the directions on the site, you have to do some mojo first.

Step 1. Run update.

sudo apt-get update

Step 2. Install apt-transport-https.