will-moore

<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

will-moore

import omero
from omero.gateway import BlitzGateway
from omero.rtypes import rint, rstring

from skimage import morphology
from skimage import measure

import argparse
import sys

will-moore

# https://forum.image.sc/t/harmonization-of-image-metadata-for-different-file-formats-omero-mde/50827/8

import omero
from omero.gateway import BlitzGateway

conn = BlitzGateway('username', 'password', port=4064, host='omero.server.org')
conn.connect()

# current group

will-moore

# -----------------------------------------------------------------------------
#  Copyright (C) 2021 University of Dundee. All rights reserved.
#
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of

will-moore

{
    "description": "test",
    "layers": [
        {
            "name": "raster",
            "type": "RASTER",
            "fileType": "ome-zarr.json",
            "url": "https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/179706.zarr"
        }
    ],

will-moore

"""
Display a 5D dask multiscale pyramid
"""

from dask import array as da
from dask import delayed
import datetime
import numpy as np
import napari
from math import ceil

will-moore

// Configure OMERO.web open_with, pointing to the script_url to this gist
// $ omero config append omero.web.open_with '["openwith_url", "https://hms-dbmi.github.io/vizarr?source=https%3A%2F%2Fs3.embassy.ebi.ac.uk%2Fidr%2Fzarr%2Fv0.1%2F$ID.zarr", {"script_url": "url/to/omero_open_with_url.js", "label":"vizarr"}]'


function getIdrIdForNode(node) {
    let idrId = node.id;
    // for testing IDR images imported to other OMERO.servers,
    // we can rename the images to be the IDR ID
    let idFromName = parseInt(node.name);

will-moore

import argparse
import sys

import omero
import omero.clients
from omero.rtypes import unwrap, rint, rstring
from omero.cli import cli_login
from omero.api import RoiOptions
from omero.gateway import BlitzGateway

will-moore

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# See https://forum.image.sc/t/omero-screens-data-import/33466/10
# and https://forum.image.sc/t/upload-issue-with-metadata-ome-xml-companion-file/59290/9

import omero.scripts as scripts
from omero.gateway import BlitzGateway
import omero

will-moore

# See https://forum.image.sc/t/searching-by-roi-comment-field-in-omero-web/38808

# Usage:
# $ python roi_comments_search.py my_search_term

import argparse
import sys

import omero
import omero.clients