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.
Tilt Series Processing
Bead Tracking on a Binned .preali File - How to track fiducials using a binned .preali file when tracking does not work properly on the full resolution image stack. This is a common problem for data acquired from the 8k camera.
Autosegmentation & Thresholding
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 a confocal image stack. These contours can then be used to calculate total nuclear volume, nuclear volume fraction, or, following manual correction, the average volume of a nucleus.
Movie Making
Creating a MPEG Video of a Tomographic Reconstruction - How to create a simple movie playing forwards and backwards through the full volume of a tomographic reconstruction using Amira.