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JEOL 4000 number 2 Specific Info

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Post-Processing Remapping the images

How to Remap the Images

Remapping the 8k images

Some quick notes of how this version differs from 4000 #1

Panel

-Ensure the FasTEM server and Stage Software are running on the left

hand side computer monitor.  This is critical as SerialEM uses these

software systems to communicate.  You simply double click "ShortCut to fastem server" and

"stage.exe"   If you are restarting it make sure these programs are not already running. 

You may have to kill these processes if they get hung.  Double click "SerialEM.exe" on the

right hand console computer.

Panel

Always flatfield.  In this case you must run the flatfield routine from

the camera panel and not from the Camera menu item. 

1) Type in the exposure time you wish to acquire your images and click "Run FlatField Routine".

2) Be patient and click all the OKs in the message boxes as it takes the various flatfields

at different bin formats.   Make sure the Tietz FastScan camera is retracted.  Chances are if the image looks funny , too dark or too bright then the Tietz camera is inserted. The tietz camera blocks the path to the 8k camera if its not retracted.

3)  After this click on Camera Setup.  Change your trial, focus, Record parameters to match

the exposure time taken.  For example if you took it at 4 seconds then set your Record to bin 1X

with exposure time 4.0 and set your Trial and Focus Parameters to 2 seconds with 2x binning for example.

NOTE:  You will always want to keep the parameters as Unprocessed and not Gain Normalized. This is not typical!  If you want Gain Normalized images just ensure the "Corrected" checkbox is checked on the Camera Panel.

Take images and check to make sure it looks good.  NO point in proceding if the images look bad.

Euccentricity

-Euccentricity on the 4000 #2 is a bit trickier.  Try your best to set it but do use the stage software

to set it.  If the euccentricity is very off then it may be best to split the tilt series into two halves.

its always better to go from the negative direction to the positive side.  For example you may

have to break it up from 0 to 50 or 60 degrees then take the other half from minus 50 to

0.  If you are starting from 0 to 60 then move the motor to say 30 degrees and adjust z until

euccentricity is achieved.  

Remapping the images:

Double click Remap.exe on the desktop or run the remap program from a

computer that has it installed.  The current software is stored in

\\firstsun.ucsd.edu\ncmirdata5\tmolina\8kremapInstall\1.0.5

Select the folder you wish to remap the tifs by clicking "Browse"

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