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

#!/usr/bin/env python

import pandas

import omero.clients
import omero.cli
import omero
import os

will-moore

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

will-moore

import argparse
import sys
import os

from omero.cli import cli_login, CLI
from omero.gateway import BlitzGateway

from omero.plugins.download import DownloadControl

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image_id,image_name,roi_id,shape_id,type,text,z,t,channel,area (µm),length (µm),points,min,max,sum,mean,std_dev,X,Y,Width,Height,RadiusX,RadiusY,X1,Y1,X2,Y2,Points
806,"Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ.dv",179764,179764,polygon,"0001-0001-0125",1,1,CENT2,0.15367967833454133,,98,631.5927124023438,2212.172119140625,103127.09680175781,1052.317314303651,409.68381187031326,,,,,,,,,,,"130,117 131,117 131,126 130,126 130,134 128,134 128,133 127,133 127,132 124,132 124,133 123,133 123,132 122,132 122,130 123,130 123,128 122,128 122,127 121,127 121,126 123,126 123,125 124,125 124,124 125,124 125,123 127,123 127,124 128,124 128,122 127,122 127,117 128,117 128,116 130,116"
806,"Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ.dv",179765,179765,polygon,"0001-0002-0127",1,1,CENT2,0.015681599830055237,,10,656.56787109375,877.3853759765625,7558.601013183594,755.8601013183594,74.44378384463185,,,,,,,,,,,"134,126 135,126 135,129 133,129 133,128 132,128 132,125 134,125"
806,"Centrin_PCNT_Cep215_20110506_Fri-1545_

will-moore

# see https://forum.image.sc/t/maximum-intensity-projection-feature-in-omero-web/54392/5

import argparse
import sys
import omero.clients
from omero.cli import cli_login
from omero.rtypes import wrap
from omero.gateway import BlitzGateway
import numpy as np

will-moore

Notes on what I installed on a new Mac M1

• Chrome
• git (via XCode)
• VS Code
• conda (Anaconda) I think from https://www.anaconda.com/products/individual#Downloads
• gpg: https://gpgtools.org/ - exported private key etc https://makandracards.com/makandra-orga/37763-gpg-extract-private-key-and-import-on-different-machine
• Slack

will-moore

# 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

will-moore

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

# 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