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Introduction to OMERO @Crick

Ken Ho

Advanced Light Microscopy STP

20 June 2022

Today's talk

Introducing you to OMERO @Crick
Overview some of the features
Basic login to OMERO and navigate
A quick look at some of your images
OMERO Pathviewer for viewing slice
OMERO figure for publishing figures
Importing images into OMERO
Aim: To get you start using OMERO

It will get you start using OMERO, but not an indepth tutorial

What is OMERO?

OMERO is a client-server database software for managing, visualizing microscopy images and associated metadata.
- Open source community driven software.
- Developed at the University of Dundee
- It stores and manages your image data
- You can find, access and share your image data and annotations with others
Crick uses OMERO Plus (Glencoe software)

client-server means that the software has 2 components, the main part sit at the server and the other part the client talks with the server and runs in other computer, laptop, etc.

This means that you can have many clients talking with the server.

Managing images with OMERO

General principle of managing image data with FAIR (Wilkinson et al., 2016)
- Findable
- Accessible
- Interoperatble
- Reuseable

Findability - images need meta-data

Image without metadata is only a set of numbers

The bubble resides at the center of the galaxy NGC 3079
NASA's Hubble Telescope, WF Planetary Camera 2
Dimensions (light years): 3,000 wide, 3,500 high Hubblesite

Mouse embryonic stem cells
Olympus microscope 60x
Pixels Size(XYZ)(µm): 0.08 x 0.08 x 0.13
Chang YW, et al., Cells, 2021 IDR image 13421281 https://idr.openmicroscopy.org/

Unfortunately, metadata are normally treated as an afterthought. It is important to provide names and terms consistently for the metadata to be useable. Therefore, it is paramount to use standardised words and terms based on one's image domain.

Findability

Attach a wide variety of meta-data to each image
Allow you to make searchable tags and fields
Recommend using consistent tags and feilds
Using standarised terms
https://idr.openmicroscopy.org/

Accessibility

OMERO can import different type of images
- .tif, .czi, .svs, .vsi, .ndpi, etc.
- bioformats v6.10.0 supported 162+ formats
View and access different image formats with one workflow

Accessibility

Fiji - OMERO connection

Fiji Fiji-omero

OMERO plugin for Fijji/ImageJ

Accessibility

QuPath - OMERO connection

Qupath Qupath-omero

QuPath OMERO extension

Accessibility by other software

Accessibility

Access using a web browser
Hands-on - login to OMERO
- URL: omero-prod.camp.thecrick.org
- Using your user ID, e.g. smithj
- Using Crick's Single Sign-ON (SSO)

OME Openmicroscopy

Accessibility

OMERO Insight application - a Desktop application
- Recommend using In-Place import image instead of Insight

omero.insight

Interoperability & Reusability

API - interoperatable with different datasets, file formats/microscopes.
- e.g. Python API, Java API, Juypter notebook

https://www.openmicroscopy.org/

OMERO + Juypter notebook

Application codes/algorithms can be attached within the image or link to github
- OMERO-prod server - image 8092
An on-demand Juypter notebook can be loaded using MyBinder or Google Colab.
- IDR example

Basic concept and navigation

Using a browser (OMERO.web app)
They are not image files anymore
- e.g. a czi slide may contain many images
No relation to CAMP's original file name/structure
Each image has an unique ID
Image name can be changed
- No impact on the original image file
Images are arranged by Dataset and Project
Each Dataset and Project also have their own unique IDs
Project and Dataset CANNOT be nested

Basic concept and navigation

Users belong to Group(s)
Members of each group can read, annotate and share data
Other users CANNOT DELETE your data
Data can only be shared within one group
To share data with other groups, new group has to be created
- Images can be OMERO-duplicate (i.e. new image IDs in OMERO) for the new group
- Actual image data are not duplicated

Basic concept and navigation

You belongs to multiple groups
- default
  - (read, write, private)
- Lab-Downward
  - (group member can read, annotate)
- Lab-Downward-oRAScle-Project
  - (some of you can read, annotate)
- Training
  - (all can read, annotate)
- Demo
  - (all can read, annotate)

Navigating Groups

OMERO.web - viewers

Viewing≠Copying
- it renders the required image part at the correct resolution on and display that on screen
- Quick respond and no need to worry transferring large data
- Great for sharing even with remote users
  - External users access via different URL
    1. show where the actual files are within CAMP

OMERO.web - viewers

Provides a few viewing options
- Image Viewer
- PathViewer - mainly for histopathology
  - OMERO Plus (proprietary)
- iviewer (to be installed)
- Figure - for publications
- Parade
- AutoTagger

Uses Sophie's TracerX slides and open PathViewer
Try open it with Image Viewer
drag, zoom, magification, rotate, etc
Check the meta data
Annotation free drawing
Export figure
PathViewer Grid to compare images

PathViewer

Browser based OMERO client for histopathology
Free-hand annotation, drawing and measurement
Continuous rotation, image flip, etc.
Supports Mask ROI
Export views and attached it back to OMERO

PathViewer GRID

Allows viewing of multiple images
- Compare slides side by side
- Sync slides - zoom, rotate them together

PathViewer and PathViewer GRID - online webinars

PathViewer
other webinars on PathViewer https://www.glencoesoftware.com/media/webinars/

OMERO figure - creating figures

OME tutorial (7 mins) https://youtu.be/mjlNBUoGKRc

OMERO image import

Storing images at OMERO is currently free
We recommend In-Place import of image data
- Raw data sit on CAMP, OMERO points to them

In-place_Import

OMERO image In-Place import

Each of you have import space at CAMP
- Mount smb://data.thecrick.org/proj-omero/
- Move (not copy) your data there for import
- Normally take a day to import
  - To ensure overnight backup is made
  - Semi-manually -> automated soon
- Raw data will be owned by OMERO server
- You can still have read access to them
If data is >5TBs please let us know in advance

Thank you

please fill out the survey below
- Feedback survey

Introduction to OMERO @Crick Ken Ho Advanced Light Microscopy STP 20 June 2022