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Test Zarr.js

Using http://guido.io/zarr.js/ to load data from a zarr file. with NO grouping (can't use the xarray zarr file used by xpublish).

Using code added to https://gitlab.com/openmicroscopy/incubator/omero-napari/-/merge_requests/1 to generate a zarr file (works with 3-channel z-stack).

$ omero napari to_zarr Image:52

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# 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

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#!/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

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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

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// 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);

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"""
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

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

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# -----------------------------------------------------------------------------
#  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

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# 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

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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