Magnification Gradient Table for Gatan US4000 CCD Camera on Tecnai F20

Chen Xu

$BrandeisEM: doc/en_US.ISO8859-1/articles-xml/mag-gradient/article.xml 1 2013-03-01 11:58:12 xuchen Exp$

Due to non-parallel beam, magnification changes along Z. This can cause enough problem if height change is big and beam is not spreat big enough. In the case of tilting series with montage, the pieces might not aligned well. Therefore, correction for magnification gradient becomes necessary.

Following the instruction from David Mastronarde, I collected montage datasets for Spotsize 1, 2 and 3 on Tecnai F20 for Gatan US4000 CCD. For each spotsize, the 3x2 montage was colleted for -60, -50, 50, 60 degree tilts under the same beam intensity. And after that, intensity series was collected at 60 degree tilt and with decreasing beam intensities. So each dataset has 12 sections with 6 pieces in each section. Specimen used is a waffle grid with Au particles on.

Analysis of the data includes run findgradient.com script twice with slightly different parameters. And final mag gradient table is then made.


montageSpot1.mgt for Spotsize 1
montageSpot2.mgt for Spotsize 2 
montageSpot3.mgt for Spotsize 3

Table of Contents
1 Mag Gradient Calibration Data Collection
2 Analysis of the Data
3 Use the Magnification Gradient Table File

1 Mag Gradient Calibration Data Collection

The data condition:

Date = Feb 12, 2013
H.T. = 200kV
Gun lens = 3
Ext.Vol. = 3950V
C2 aperture = 100um
Obj. aperture = 40um
Mag = 19000X 
binning = 4

2 Analysis of the Data

SpotSize 1

SpotSize 2

SpotSize 3


3 Use the Magnification Gradient Table File

Here is the information from David's instruction.

“ The mag gradient table should go in /usr/local/ImodCalib/Distortion or a subdirectory thereof. Then on the eTomo setup page, when you press the button to open a file chooser for a mag gradient file, the chooser will open in this directory. ”