gladlab-ip

A simple process automation tool created by the Gladfelter lab at UNC Chapel Hill to streamline fungal cell biology data analysis.

When working with microscopy data, the pain points for the lab are:

1. organizing the data due to its large size
2. adapting the data to 3rd party tools given its proprietary *.nd2 format
3. cropping ROIs given the complex, inter-weaving cells

The tool crawls through folders of *.nd2 files and caches max projections of each z-stack ahead-of-time. When ready, the user can launch a local web interface to manually lasso-select ROIs that are cropped, padded, and dumped into more-accessible *.TIFF files.

demo example

tablet mode

The web interface shows a QR code so that the user can draw these ROIs on a tablet if they so choose.

installation and usage

Refer to the gladlab-ip wiki.