PlateViewer

BigDataViewer based Fiji plugin for visual inspection of (multi-well) high throughput microscopy image data.

Features:

• lazy loading of image data for interactive browsing
• support for multi-resolution image data
• segmentation (label mask) visualisation
• linked table, scatterplot and image browsing
• shared coloring model of table scatterplot and image overlay
• integrated (right-click) github issue reporting for efficient collaborative discussion of imaging or image analysis issues
  • automated reporting of plate, well and site as well as automated screenshot generation
  • see example issues here

Future directions:

• explore whether one could develop standardised CellProfiler segmentation images and table outputs that could be directly visualized with this tool.

Usage examples

The plugin has been heavily used in a Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera. Below screenshots show data from this study.

Plate view

Well view

Site view

Cell segmentation view

Install

• Please install Fiji
• Within Fiji, please enable below Update Site:
  • PlateViewer
• Restart Fiji

Run

• The plugin can be started at [ Plugins > PlateViewer > PlateViewer... ]
• Most efficiently, just type Plate into the Fiji search bar and hit [ Run ]:
• You will be presented with below user interface:
  • Plate images directory: The folder containing all the images of one plate.
  • Include sub-folders: Sometimes the images are stored into some nested sub-folder structure. If this is the case, please check this option (e.g., for the ALMF-EMBL screening naming scheme). If your images are not in sub-folders, please do not check this to save time parsing all files and exclude parsing wrong files (e.g., for the batchHdf5 naming scheme).
  • Only load files matching: Regular expression to subset your files. Typical choices are .*.h5 or .*.tif
    • Please note that it must be .* (and not only a *) to match anything.
  • Load image table: (Advanced) Check this if you also want to load an associated table, where each row contains information about one image on the plate.

Usage instructions

There is more information to come here, but please explore left and right clicking into the different visualisations.

Supported file naming schemes

We currently onlly support a number of limited file naming schemes. If you need support for a different naming scheme, please write an issue.

ALMF-EMBL (wells and sites)

MD (wells and sites)

Cite

This github repository can be cited (registered at ZENODO):

• Tischer, C., and R. Pepperkok (2019) PlateViewer: Fiji plugin for visual inspection of high-throughput microscopy based image data. https://doi.org/10.5281/zenodo.3522688