fiji / microscope-image-quality

This project is an ImageJ plugin for Google's microscope image focus quality classifier.

Publication

Yang, S. J., Berndl, M., Ando, D. M., Barch, M., Narayanaswamy, A. , Christiansen, E., Hoyer, S., Roat, C., Hung, J., Rueden, C. T., Shankar, A., Finkbeiner, S., & and Nelson, P. (2018), "Assessing microscope image focus quality with deep learning", BMC BioInformatics 19(1).

Quickstart

Assuming you already have Apache Maven installed:

mvn -Pexec

Instructions for installing Apache Maven might be as simple as apt-get install maven on Ubuntu and brew install maven on OS X with homebrew.

See the ImageJ Development page for further details.

Installation in Fiji

If you have Fiji installed and want to incorporate this plugin into your installation:

# Set this to the path there Fiji.app is installed
FIJI_APP_PATH="/Users/me/Desktop/Fiji.app"
mvn -Dimagej.app.directory="${FIJI_APP_PATH}"

Then restart Fiji and search for "quality", or navigate to Plugins › Classification › Microscope Image Focus Quality in the menu.