Why to monitor
microscope condition?

Microscopes are sophisticated optical instruments that take extremely precise measurements on biologic samples. Therefore, it is essential not only to keep them in good condition but also to know what their condition is.

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. Ensure that performance degradation is detected as soon as possible
  2. Help the core staff to diagnose the problem and react accordingly
  3. Provide evidence serving in the dialogue with microscope manufacturers and service providers
  4. Calibrate hardware
  5. Provide quality assurance and analysis data and meta-data to the users of the facility

When to monitor
microscope condition?

The monitoring of the microscope condition should be done at different moments to ensure that the equipment is performing according to a predefined specifications chart.

  • During the installation of new equipment to ensure the acceptance of the installation and establish the baseline for the future.
  • During the service life of the system:
    • after the periodic maintenance is carried out either by the core facility staff or by an external service provider.
    • when there is a doubt about the performance of the equipment.
    • when there is a change in the equipment or its environment.

OMERO-metrics is a new web tool
for microscope performance monitoring

OMERO-metrics aims to provide a comprehensive solution for monitoring the performance of microscopes.

  • It draws on the experience of MetroloJ-QC: it is tested
  • uses the OMERO platform to store and manage metrology data: it is FAIR
  • uses OMERO-web’s visualization capabilities to provide an interface: it is user-friendly

How does it work?

  1. First time configuration of the analysis you want to perform
  2. Import images into OMERO in a well defined structure
  3. Run the analysis using the pre-configured parameters
  4. Visualize the results in a dashboard

UML diagram

If you whish to see the UML diagram, here it is:

flowchart LR
    C0[Create project]
    T1[Select project]
    T2{has config?}
    C1[Create config]
    V3[Render timecourse view]
    V4[Render add datasets view]
    T1 --> T2
    T2 -- no --> C1
    T2 -- yes --> V2
    subgraph CONFIGURATION
    C1 --> T2
    end
    subgraph IMPORT
    end
    subgraph RUN
    end
    subgraph VISUALIZE
    V2{has datasets?}
    V2 -- yes --> V3
    V2 -- no --> V4
    end

1. 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

2. Import image data into OMERO

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

2.1. Importing images

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

3. Run the analysis

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

3.1. Run the analysis

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

3.2. Parametrize the analysis

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

4. Visualize the results

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

4.1. Group level

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

4.2. 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.

4.3. 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.

4.4. 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
  • FBI-data: Guillaume
  • Project responsible: Julio
  • Project developer: Oumou
  • WG-microscope-metrics: WGMM
    • Dauphin Aurelien
    • 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