As an intern at the Allen Institute for Brain Science, I worked on image acquisition automation and image processing. These are some of the results of this effort.
Added trajectory velocity and acceleration capabilities for the Focus Axis, in the Zeiss device adapter for Micro-Manager
Goal: find a sample on a slide (using thresholding and an automated routine), acquire z stacks of each x,y coordinate at an appropriate depth (determined using Sobel gradient), create a minimum intensity projection (MIP), and put these in an appropriate format to then be passed into Tera Stitcher.
a close-up of a MIP of neurons
a close-up of neurons imaged at only one plane
Goal: Integrate 20x automation into a routine which can image multiple slides without human intervention
Goal: Get user input and acquire a z-stack, both stitching images within the boundaries given as input, and putting them in an appropriate format for tera stitcher