About Me
E-mail: a3perez at ucsd dot edu
Personal E-mail: alexjperez at gmail dot com
IMOD Tutorials
Creating TIFF series of ZaP window with segmentations in IMOD - How to create an output series of TIFF images of every slice of an MRC volume with segmentations displayed. Useful for testing autosegmentation algorithms.
Autosegmentation & Thresholding Tutorials
Autosegmentation of Nuclei from a DAPI-labeled Confocal Stack - An automated thresholding approach that uses the image processing package Fiji to yield contours around all DAPI-labeled nuclei from confocal image stacks. These contours can then be used to calculate total nuclear volume, nuclear volume fraction, or, with manual correcting, the average volume of a nucleus.