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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
@will-moore
will-moore / ngff_plate_segment_add_labels.py
Created April 27, 2022 15:00
process all the images in an OME-NGFF plate, segmenting them and adding OME-NGFF labels to each image
import os
import zarr
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label
from skimage.morphology import closing, square
from ome_zarr.io import parse_url
@will-moore
will-moore / copy_annotations.py
Created March 28, 2022 11:31
OMERO cli script to copy annotations from an Image to another
# https://forum.image.sc/t/how-to-copy-the-metadata-set-of-an-image-and-paste-it-to-a-new-one/60357
import argparse
import sys
import omero
import omero.clients
from omero.cli import cli_login
from omero.gateway import BlitzGateway