Minimal dataset & code for proof of concept - Argoslide - Fiji - OMERO

An open-source workflow for assessing light microscope performance using a single micropattern.

Romain Guiet, Thierry Laroche, José Artacho, Nicolas Chiaruttini, Olivier Burri, Arne Seitz

The growing need for reliable quantitative measurements in light microscopy has been identified by the community recently and led to the creation of an initiative called  Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMI). One of the aims is to push for the creation of simple, direct, reliable and widely adoptable instrument quality controls. This serves for defect detection, continuous proof of the instrument's ability to reliably produce quality imaging data, and the possibility to compare performance across devices. 

By lowering the learning curve for facilities and laboratories through simple robust protocols and as-automated-as-possible open source image processing, we produced a workflow for the acquisition and measurements of typical light microscope metrics using a single pattern from a commercially available ArgoLight-SIM slide. Through a fully automated workflow in Fiji, we can measure axial resolution (FWHM ), inter-channel co-registration (Pearson's Correlation Coefficient), field uniformity (local intensities) and field distortion (comparing spatial localization with respect to a simulated pattern) at multiple positions across the field of view, in a single image. 

Moreover, in order to ease bookkeeping, an OMERO database is used as a backend to store the acquired images, metadata, as well as the resulting metrics and reports. These reports in turn can be used within OMERO Parade to follow instrument performance changes. This workflow is built on open-source software and will facilitate  the assessment of instrument quality over time with minimal effort.

  == INPUTS ==
  Images to upload and analyse , a template image to find rings ( available : https://doi.org/10.5281/zenodo.6597338)
  OMERO : 
   - an active user 
   - a project , please project ID at "argoslide_project_ID" (see below)
   - a dataset, name .LSM980.
  
  == OUTPUTS ==
  Upload images on OMERO, 
  Compute metrics and add them into an OMERO table
  Add tags to uploaded images
  
  = DEPENDENCIES =
   - omero-simple-client.jar : https://github.com/GReD-Clermont/simple-omero-client
  update site :
   - IJ-OpenCV 
   - Multi-Template-Matching