General IMOD Tutorials
|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.|
TEM Tomographic Processing Tutorials
|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.|
JEOL 4000EX #1 and #2
|4/6/2012||Maximum Intensity Projections in Amira||How to create a MPEG movie of a tomographic reconstruction featuring a maximum/minimum intensity projection of the volume using Amira. The movie first plays through the reconstruction in one direction, then plays backwards while zooming in on a feature of interest, then plays the opposite direction while fading into the maximum intensity projection, which is then displayed and rotated.|
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.
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.