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Image acquisition routine for the Scanning Lab at the Allen Institute for Brain Science

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Rapid Stacks

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.

Micro-Manager

Added trajectory velocity and acceleration capabilities for the Focus Axis, in the Zeiss device adapter for Micro-Manager

Python scripts

20x acquisition

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.

an example 20x MIP image

an example 20x DAPI image

a close-up of a MIP of neurons

a close-up of neurons imaged at only one plane

Multi-slide acquisition

Goal: Integrate 20x automation into a routine which can image multiple slides without human intervention

63x acquisition

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

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Image acquisition routine for the Scanning Lab at the Allen Institute for Brain Science

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