Why to monitor
microscope condition?

Microscopes are scientific measuring devices, so it is crucial to:

  • Preserve them in good condition
  • Track their current condition

Every careful measurement in science is always given with the probable error […] every observer admits that he is likely wrong, and knows about how much wrong he is likely to be.

Bertrand Russell

Key objectives
when monitoring microscope condition

  1. Detect performance issues early
  2. Support core staff in diagnosing and responding
  3. Provide evidence for discussions with manufacturers
  4. Calibrate hardware
  5. Deliver quality assurance data and metadata to:
    • stakeholders
    • users
    • scientific community

When to monitor
microscope condition?

Microscope condition should be monitored at key times to ensure performance meets predefined specifications:

  1. At installation:
    • Confirm acceptance
    • Establish baseline
  2. During service life:
    • After periodic maintenance (by staff or external providers)
    • If performance issues arise
    • When equipment or environment changes

What is OMERO-metrics?

OMERO-metrics offers a complete solution for monitoring microscope performance.

  • Built on the trusted MetroloJ-QC experience
  • FAIR data management via OMERO
  • User-friendly visualization through OMERO-web

but also for reproducibility
and recognition of core facility staff

How is OMERO-metrics built?

Explore the Tools

microscopemetrics-schema

microscopemetrics-schema

microscope-metrics

omero-metrics

How does it work?

  1. First time configuration of the analysis
  2. Import images into OMERO in a well-defined structure
  3. Run the analysis
  4. Visualize the results in the dashboard

1. Core concepts

1.1. Embracing the ISA model

The ISA model organizes metadata into three levels:

  • Investigation / Group:
    the instrument/microscope
  • Study / Project:
    the analysis type (e.g., 20x field homogeneity)
  • Assay / Dataset:
    the measurements linked to raw images

DEMO

2. Configure the analysis

The first step, and only to be the first time, is to configure the analysis that you plan to run.

  • Create a new OMERO Project for every analysis you want to perform
  • For each Project/Analysis define its type
  • Once the analysis type is chosen, define the parameters that will be used to run the analysis using a form
  • Save the parameters

3. Import image data into OMERO

OMERO is a server-client platform for managing, visualizing, and analyzing microscope images and metadata.

3.1. Importing images

Acquired images are imported into OMERO following a well-defined structure.

4. Run the analysis

Now that the images are imported into OMERO, the next step is to run the analysis.

4.1. Run the analysis

If a dataset has not been analyzed yet, the user will have the possibility to trigger the analysis.

4.2. Parametrize the analysis

The user will be able to parametrize the analysis defaulting to the parameters defined in the configuration step.

5. Visualize the results

OMERO-metrics provides a dashboard to visualize the results of the analysis at different levels.

5.1. Group level

At the group level, the user will be able to see a summary of the status of the microscope.

5.2. Project level

At the project level, the user will be able to see the results of the analysis for all the datasets in the project. The user will be able to browse, across time, the results of the analysis.

5.3. Dataset level

At the dataset level, the user will be able to see the results of the analysis for all the images in the dataset, providing a more detailed view of the state of the microscope at that time.

5.4. Image level

At the image level, the user will be able to see the results of the analysis for a single image.

Attributions

  • FBI-core facility integration Cedric Mathews
  • FBI-data: Guillaume Gay
  • Project responsible: Julio Mateos Langerak
  • Project developer: Oumou Dhmine, Julio Mateos Langerak
  • WG-microscope-metrics: WGMM
    • Aurelien Dauphin
    • Sylvain Derossi
    • Audrey Salles
    • Erwan Grandgirard

Documentation

Further documentation will come soon at https://microscopemetrics.readthedocs.io

Licensing

The code is distributed as open source under GPL 3.0. The main reason being that it is the license used by the OME consortium.

References

[1] Cédric Matthews and Fabrice P. Cordelieres, MetroloJ : an ImageJ plugin to help monitor microscopes’ health, in ImageJ User & Developer Conference 2010 proceedings.

[2] Theer, P., Mongis, C. & Knop, M. PSFj: know your fluorescence microscope. Nat Methods 11, 981–982 (2014). doi.org/10.1038/nmeth.3102

[3] argolight.com/measure-microscopes-performances-detect-issues-with-daybook