Overview
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A page of terms that are used often in backprojection / electron tomography work.
Glossary of Terms
A
- .ali: A .mrc format file created and used in etomo / IMOD. Specifically, it is an aligned image stack whose alignment is based on cross correlation, optional manual correction by midas, optional fiducial tracking and tomo pitch correction. This file is what the .rec file will be backprojected from.
E
- EM: Electron Microscope
H
- HVEM: High Voltage Electron Microscope. Acelerated voltage is set to 1 meV
I
- IVEM: Intermediate Voltage Electron Microscope. Accelerated voltage is between 200 and 400 keV. Examples of IVEMS: JEOL 4000, JEOL 3200, FEI Titan
P
- Postmag: A value given to the change in magnification from an EM image due to the distance between the viewing window and the CCD / negative holder box. The greater the distance, the greater the value of the postmag.
R
- Rawtlt (rawtilt): Usually a file or handwritten list of tilt angles, indicating the exact angle of tilt for a particular tilt series dataset. Necessary for backprojection.
- .rec: A .mrc format file created and used in etomo / IMOD. Specifically, it is the backprojected slice by slice volume.
S
- segmentation: a method for visualizing 3D data. Taking a slice by slice volume, whether EM or LM, an agent (human or machine algorithm) traces out structures of interest and renders the tracings as 3D models, typically as a triangle mesh model.
- ssh: A secure method of logging into another machine. To use, open a terminal window and type the following suggested line: ssh -Y [username]@[machinename]. The name of the machine that you can log into along with a preset username / password will be required to ssh. For more information about ssh, click here .
T
- Tilt series: A set of images usually acquired using a TEM where an object placed inside of the TEM has been tilted over some range (typically -60 degrees to +60 degrees with 2 degree tilt increments). Usually is then sent to be processed for backprojection.
- Tomogram: A set of slices that make up some 3D sample or object. Informal Synonyms: Volume
- Tomography: imaging by sections or sectioning. Images can be acquired by physical sectioning e.g. serial section tomography or by digital means e.g. backprojection.
- Tomopitch: The alignment correction step where the user corrects for the angle / pitch in the y/z dimension.
V
- Volume: for tomography, an image set with an x, y and z component e.g. a slice by slice backprojection. Not to be confused with image sets such as a tilt series as these are a set of images with no corresponding z information. Typically has a .rec or .out extension.