BigDataViewer based Fiji plugin for visual inspection of (multi-well) high throughput microscopy image data.
Features:
Future directions:
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 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
.*
(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.There is more information to come here, but please explore left and right clicking into the different visualisations.
We currently onlly support a number of limited file naming schemes. If you need support for a different naming scheme, please write an issue.
This github repository can be cited (registered at ZENODO):