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

# 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

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

import argparse
import sys
import os

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

from omero.plugins.download import DownloadControl

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

#!/usr/bin/env python

import pandas

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

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