Querying metadata from omero in python

A colleague needed a table listing image ID, image filename, and number or ROIs for all images in a project. Here’s the python script I came up with: Query Metadata from omero Imports import omero from omero.gateway import BlitzGateway import pandas as pd import getpass Connect to omero conn = BlitzGateway('XXXXX', getpass.getpass(), host='omero.server.org') conn.connect() ········ True Retrieve datasets This sets up an iterator over the needed datasets but does not load any data into memory (yet). [Read More]

Importing data to OMERO

Getting your data into the database is one of the most frequent tasks when working with OMERO. There are two different ways to import data into OMERO: Via the desktop app OMERO.insight or via the commandline client that comes with OMERO.py. Both software packages can be found on the OMERO download site https://www.openmicroscopy.org/omero/downloads/. While the desktop app is easy and intuitive to use, a drawback of using it is that it must remain open while the data is uploaded. [Read More]

Omero bulk annotation

Edit May 21 2021 I made a short video presentation on the subject, as a “flash” talk for the OME Community Meeting 2021: https://youtu.be/inGQXtbzoZI . Summary This tutorial gives a step-by-step instruction on annotating containers (Projects, Datasets, Plates, or Screens) and individual or multiple images. In particular, we show how to annotate selected images in batch mode using spreadsheet documents as a convenient method to record metadata during or after an experiment. [Read More]