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General IMOD Tutorials


Creating TIFF series of ZaP window with segmentations

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
3/29/2012Bead 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


Amira Tutorials
4/6/2012Maximum 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.


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.







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