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will-moore / ome_zarr_converter.py
Last active November 7, 2025 11:27
# conda activate kong_idr
# pip install alpineer
# Successfully installed alpineer-0.1.13 charset-normalizer-2.1.1 contourpy-1.3.3 cycler-0.12.1 fonttools-4.60.1 imageio-2.37.0
# kiwisolver-1.4.9lazy-loader-0.4 matplotlib-3.10.7 natsort-8.4.0 networkx-3.5 numpy-1.26.4 packaging-25.0 pandas-2.3.3 pillow-12.0.0
# pyparsing-3.2.5 python-dateutil-2.9.0.post0 pytz-2025.2 scikit-image-0.25.2 scipy-1.16.2 six-1.17.0 tifffile-2025.10.16 tzdata-2025.2
# xarray-2025.10.1 xmltodict-0.13.0
# pip install zarr
@will-moore
will-moore / OMERO.figure_NGFF_demo.json
Last active March 28, 2025 09:12
Test figure.json for https://github.com/ome/omero-figure/pull/619
{
"version": 8,
"panels": [
{
"x": 32.776939633609516,
"y": 299.60384546911166,
"width": 157,
"height": 160.5839416058394,
"zoom": 100,
"dx": 0,
@will-moore
will-moore / SSBD_zarr_samples.csv
Last active June 23, 2023 11:55
OME.Zarr sample list from SSBD
SSBD Project ID SSBD Dataset ID license URL Date added
2-Kyoda-WormEmbryoRNAi wt_N2_030303_01 CC BY-SA https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/wt-N2-030303-01.zarr 2023-03-22
98-Morita-ToothEpiCellDev fig2ab_trajectory_epithelialcell CC BY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/fig2ab_trajectory_epithelialcell.zarr 2023-03-22
48-Susaki-MouseBrainCUBIC Fig3A_R26-pCAG-nuc-3xmKate2 CC BY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3A_R26-pCAG-nuc-3xmKate2.zarr 2023-03-22
48-Susaki-MouseBrainCUBIC Fig3C_H2B-mCherry CC BY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3C_H2B-mCherry.zarr 2023-03-22
48-Susaki-MouseBrainCUBIC Fig3D_H2B-EGFP CC BY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3D_H2B-EGFP.zarr 2023-03-22
48-Susaki-MouseBrainCUBIC Fig3E_Thy1-YFP-H CC BY https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig3E_Thy1-YFP-H.zarr 2023-03-22
199-Ichimura-MulticellularDyn Fig2_BrainSliceRGB CC BY-NC https://ssbd.riken.jp/100118-dcacbb41/zarr/v0.4/Fig2_BrainSliceRGB.zarr 2023-03-2
@will-moore
will-moore / inplace_fileset4.py
Created April 4, 2023 10:16
import argparse
import os
import sys
import omero.clients
from omero.cli import cli_login
from omero.rtypes import rstring, rlong
from omero.gateway import BlitzGateway
@will-moore
will-moore / inplace_fileset3.py
Last active April 3, 2023 16:33
import argparse
import os
import sys
import omero.clients
from omero.cli import cli_login
from omero.rtypes import rstring, rlong
from omero.gateway import BlitzGateway
@will-moore
will-moore / replace_fileset2.py
Created March 31, 2023 13:50
# see https://github.com/IDR/idr-metadata/issues/652
import argparse
import os
import sys
import omero.clients
from omero.cli import cli_login
from omero.model import ChecksumAlgorithmI
from omero.model import NamedValue
@will-moore
will-moore / inplace_fileset.py
Created March 7, 2023 17:11
import argparse
import locale
import os
import platform
import sys
import omero.clients
from omero.cli import cli_login
@will-moore
will-moore / replace_fileset.py
Created February 23, 2023 17:57
OMERO: Upload files in a directory to create a new Fileset to replace an existing Fileset
import argparse
import locale
import os
import platform
import sys
import omero.clients
from omero.cli import cli_login
from omero.model import ChecksumAlgorithmI
@will-moore
will-moore / omero_viewer.html
Created September 27, 2022 22:14
Minimal viewer based on webgateway image viewer
<html>
<!-- See https://forum.image.sc/t/omero-embedded-onto-html-pages-in-moodle/72047 -->
<head>
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no">
<link rel="stylesheet" type="text/css" href="https://omero.mvls.gla.ac.uk/static/webgateway/css/ome.viewport.css?_5.8.1" media="all" />
<link rel="stylesheet" type="text/css" href="https://omero.mvls.gla.ac.uk/static/webgateway/css/ome.toolbar.css?_5.8.1" media="all"/>
<link rel="stylesheet" type="text/css" href="https://omero.mvls.gla.ac.uk/static/webgateway/css/ome.gs_slider.css?_5.8.1" media="all" />
<link rel="stylesheet" type="text/css" href="https://omero.mvls.gla.ac.uk/static/webgateway/css/base.css?_5.8.1" media="all" />
@will-moore
will-moore / plate_rename_images.py
Created September 16, 2022 09:12
rename images in a Plate in OMERO
# https://forum.image.sc/t/imports-of-tiff-to-omero/71648/9
# usage: with plate ID - You will be asked for login...
# $ python plate_rename_images.py 1234
import argparse
import sys
from omero.cli import cli_login
from omero.gateway import BlitzGateway