Microscope Slide Screener

The Joint Genome Institute (a DOE collaboration affiliated with LBL) was using Ciona instestinalis (sea squirts) to investigate gene regulatory networks. These animals are ideal because transgenic DNA is easily introduced and their larval stage exhibits a prominent notochord. Larval stage samples were mounted on ordinary microscope slides and stained to reveal gene expression. The JGI wished to have a machine that could optically review 100 slides per day and detect/screen samples of interest for later study by a human operator.

Our machine integrates a slide loader, an XY stage, a Zeiss motorized microscope, a Nikon digital camera, a barcode reader, several "light-curatain" sensors, a personal computer and custom software. In addition to controlling the whole system, our software uses a commercial image processing program to do detailed analysis of each image. Our software also downloads and uploads data to the large commercial databases maintained at JGI.

The result is a system that can do the laborious work of scanning large amounts of slides while returning to the user only the most relevant data to examine and save. This work was done with my colleague Zach Radding.