The SerialEM Script Repository

Scripts by Category

Calibrations

• TuneScope (Wim Hagen)
• Titan IlluminatedAreaLimits (Guenter Resch)
• CLcomp_shift_angle_alignment JEOL CryoARM300 (Marcus Fislage)
• Find Tilt Axis Offset (Guenter Resch)
• BTandSTIGvsISmeasure CryoARM300 (Marcus Fislage)
• BeamTilt vs IS CryoARM300 (Marcus Fislage)

High-Level Functions

• k3blackstripecheck (Wim Hagen)
• Wait For Drift (Juha Huiskonen)
• Save Microscope State (Guenter Resch)
• Map grids (advanced) (Christian Dienemann)
• Hole Pattern Directions CryoARM300 (Marcus Fislage)
• Center Beam (Juha Huiskonen)
• MapGrids (Wim Hagen)
• k2blackstripecheck (Wim Hagen)
• Refine Eucentricity with Threshold (Guenter Resch)
• Center Detail (Juha Huiskonen)
• Focus Pair (Juha Huiskonen)
• Restore Microscope State (Guenter Resch)
• Make Grid Alas JEOL CryoARM300 (Marcus Fislage)

Tomography

• Measure Eucentric Height Alternative (Georges Chreifi)
• Grouped dose-symmetric tomography (Wim Hagen)
• PACE-tomo target selection (Fabian Eisenstein)
• Jensen lab FISE (Georges Chreifi)
• Pre-calibrations for FISE tomography (Fabian Eisenstein)
• Dose-symmetric tomography (Wim Hagen)
• Parallel cryo electron tomography (PACE-tomo) (Fabian Eisenstein)
• Jensen lab FISE Calibrations (Georges Chreifi)
• Fast-Incremental Single-Exposure tomography (Fabian Eisenstein)
• Find Tilt Range (Martin Schorb)
• Quick Tomography (Martin Schorb)

Single Particle

• Parameters Script JEOL CryoARM (Marcus Fislage)
• test hole centering (Wim Hagen)
• LD (Henning Stahlberg)
• Manual Acquisition (Juha Huiskonen)
• Intensity Zero (Jan Rheinberger)
• Set Target for Sample Thickness (Jan Rheinberger)
• Test shots JEOL CryoARM300 (semi-automated) (Marcus Fislage)
• SPA multiple images (Wim Hagen)
• SPA data collection on JEOL CryoARM300 (Marcus Fislage)
• Parameters (Henning Stahlberg)
• SPAK2aligntomap (Wim Hagen)
• Tilt Pair (Juha Huiskonen)
• Auto Acquire on Holey Carbon (Juha Huiskonen)
• Measure Sample Thickness (ALS) (Jan Rheinberger)
• Measure Sample Thickness (Jan Rheinberger)
• Functions for JEOL CryoARM300 (Marcus Fislage)
• SPA multiple images Test Radius (Wim Hagen)
• Measure Sample Thickness (LM) (Jan Rheinberger)
• Zero Loss Settings (Jan Rheinberger)

Other Data Acquisition

• CRmov (Jason de la Cruz)
• Check grid (Jason de la Cruz)
• Random Grid Sampler (Guenter Resch)
• Serial Section Maps (Martin Schorb)
• Prepare gridsquare (set eucentric height) (Jason de la Cruz)
• Acquire image SPIRAL (Francisco Javier Chichón)
• Continuous image acquisition (Jason de la Cruz)

Function Libraries

• WaitForRefilling (Chen Xu)
• CINAAutoFocus (Henning Stahlberg)
• CINACronJob (Henning Stahlberg)

Testing

• Beam Intensity Calibration Test (Guenter Resch)
• Python Test (Guenter Resch)
• Set intensity value (condenser lens) (Jason de la Cruz)
• K2 alignment timing test (David Mastronarde)
• SerialEM Snapshot (Guenter Resch)
• Probe intensity value (condenser lens) (Jason de la Cruz)