IMOD Tutorials
 | 2/20/2012 | How to create an output series of TIFF images of every slice of an MRC volume with segmentations displayed. There does not seem to be a good way to do this through the command line. The output from this method has been used to test autosegmentation algorithms for cell nuclei. | |
 | 3/29/2012 | Bead Tracking on a Binned .preali File | A method for achieving accurately tracked fiducials when the tracking process does not work properly on the full resolution image stack. This is a common problem for data acquired from the 8k x 8k camera. This method takes advantage of running the IMOD program beadtrack through the command line on a significantly binned version of the input stack. Its output is recognized by eTomo for ease of subsequent processing steps. |
Amira Tutorials
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.