DE_Continuous_Rotation_Tomography.txt

ScriptName DE_Continuous_Rotation_Tomography
# For SerialEM-controlled continuous stage rotation and
# simultaneous mode movie recording for tomography.

# License ISC: Internet Software Consortium license,
# http://opensource.org/licenses/ISC

# Written by Benjamin Bammes (bbammes@directelectron.com),
# Isaac Forrester (isaac.forrester@bcm.edu), and Erik Anderson
# (erik.anderson@bcm.edu).

#################
## IMPORTANT ##
#################

# Ensure that Record mode has Frame Saving enabled!

# Check the e/physpix/s over an empty area using Record and
# enter the value for "eps" in the OPTIONS setting.

# Checking microscope alignment, coma-free 

# Set the other OPTIONS parameters as desired.

# The Dose options are in units of e/A2.

# totalDose includes the zeroDegDose.

# Tilt angles are given in degrees.

# Tilting starts at 0 degrees and goes up to maxDeg, then
# tilting starts at overlapDeg and goes down to minDeg.

# tiltingDelay is the time between issuing the TiltDuringRecord command
# and the stage tilt beginning. This delay seems to be somewhat variable,
# even on the same microscope, so set this to the minimum observed
# delay so that the recorded movie does not miss the beginning of stage
# rotation.

##############
## OPTIONS ##
##############

eps = 23.15
defocus = -5
zeroDegDose = 20
totalDose = 120
minDeg = -60
maxDeg = 60
overlapDeg = 2
extraTime = 0.5
tiltingDelay = 1.55

###################
## GET SETTINGS ##
###################

ReportBinning R
binningValue = $reportedValue1
ReportCurrentPixelSize R
apixPhys = $reportedValue1 * 2 / $binningValue

###################
## CALCULATIONS ##
###################

doseRate = $eps / ($apixPhys * $apixPhys)
zeroDegTime = $zeroDegDose / $doseRate
tiltingTime = ($totalDose - $zeroDegDose) / $doseRate
tiltingSpeed = (($maxDeg - $minDeg + $overlapDeg) / $tiltingTime - 0.037) / 29
posDelay = ($tiltingDelay + $zeroDegTime) * 1000
posTime = $zeroDegTime + $tiltingTime * $maxDeg / ($maxDeg - $minDeg + $overlapDeg) + $extraTime
negDelay = $tiltingDelay * 1000
negTime = $tiltingTime * ($overlapDeg - $minDeg) / ($maxDeg - $minDeg + $overlapDeg) + $extraTime
degPerS = ($maxDeg - $minDeg + $overlapDeg) / $tiltingTime

############
## SCRIPT ##
############

echo
echo ================================
echo DE_Continous_Rotation_Tomography
echo

echo Defocus = $defocus um
echo Physical pixel size = $apixPhys A/pix
echo Super-resolution binning factor = $binningValue
echo Exposure rate on camera = $eps e/physpix/s
echo Initial zero deg exposure = $zeroDegDose e/A2
echo Total exposure = $totalDose e/A2
echo Minimum tilt angle = $minDeg deg
echo Maximum tilt angle = $maxDeg deg
echo Overlap angle = $overlapDeg deg
echo Extra time = $extraTime s
echo TiltDuringRecord delay = $tiltingDelay s
echo Exposure rate = $doseRate e/A2/s
echo Initial zero deg time = $zeroDegTime s
echo Total tilting time = $tiltingTime s
echo Tilt speed setting = $tiltingSpeed
echo Tilt speed = $degPerS deg/s
echo Positive direction tilt delay = $posDelay ms
echo Positive direction exposure time = $posTime s
echo Negative direction tilt delay = $negDelay ms
echo Negative direction exposure time = $negTime s
echo

ResetClock

ReportFrameBaseName
baseName = $reportedValue2

ScreenUp
SetBeamBlank 1
SetColumnOrGunValve 1
TiltTo 0

CameraProperties
echo Camera physical pixel size is $reportedValue4 um
ReportMag
echo TEM magnification is $reportedValue1 x
ReportSpotSize
echo TEM spot size is $reportedValue1
ReportPercentC2
echo TEM illumination C2 is at $reportedValue1 percent

echo Loading record mode settings...
SetDoseFracParams 1 1 0 0 1
SetFrameTime R 0.016

echo Autofocusing...
GoToLowDoseArea F
AutoFocus 1
SetDefocus $defocus_val

echo Acquiring view mode for re-aligning...
GoToLowDoseArea V
V
Copy A H

echo Setting eucentricity...
GoToLowDoseArea V
Eucentricity 6

echo Initializing tilting direction to positive...
TiltTo -10
Delay 2 s
TiltTo 0

echo Autofocusing...
GoToLowDoseArea F
AutoFocus 1

echo Realigning...
GoToLowDoseArea V

V
AlignTo H

echo Going to record mode...
GoToLowDoseArea R
SetDefocus $defocus
Delay 5 s

echo Acquiring positive tilt direction...
GoToLowDoseArea R
Delay 5 s
SetExposure R $posTime 0
SetFrameBaseName 1 1 -1 $baseName_pos
TiltDuringRecord $maxDeg $posDelay $tiltingSpeed
SetFrameBaseName 1 1 -1 $baseName

echo Tilting back to near zero...
TiltTo $overlapDeg

echo Realigning...
GoToLowDoseArea V
V
AlignTo H

echo Acquiring negative tilt direction...
GoToLowDoseArea R
Delay 5 s
SetExposure R $negTime 0
SetFrameBaseName 1 1 -1 $baseName_neg
TiltDuringRecord $minDeg $negDelay $tiltingSpeed
SetFrameBaseName 1 1 -1 $baseName

echo Tilting back to zero...
TiltTo 0
SetBeamBlank 1

ReportClock

echo Acquisition complete

echo ========================================
echo