Technical expertise

Data acquisition on TFS Titan Krios, TFS Talos Arctica, FEI Polara and FEI TECNAI Spirit

• Tomogram acquisition with TFS Xplore 3D (FEI TECNAI Spirit)

• SerialEM scripting and automation for automated tomogram acquisition

Tomogram reconstruction and subtomogram averaging

• etomo/PEET

• EMAN2

• AreTomo

• Dynamo

Tomogram segmentation

• 3dmod

• Amira

• ORS Dragonfly (use of Unets)

• EMAN2 (use of convolutional neural networks)

Data acquisition on TFS Titan Krios, TFS Talos Arctica

• micro-ED acquisition with EPU-D, Delphi and SerialEM

• SerialEM scripting and automation for automated micro-ED data acquisition

Indexing - Integration - Phasing - Refinement

• XDS

• Phenix

• COOT

Gallium FIB milling

• TFS Aquilos

• TFS Versa 3D Dual-Beam

Plasma FIB milling

• TFS Hydra

Automated milling

• TFS AutoTEM

• Autolamella

  • Article: https://www.sciencedirect.com/science/article/pii/S104784772030054X?via%3Dihub

  • Github: https://github.com/DeMarcoLab/autolamella

• TFS Autoscript

• Proficient at TFS Autoscript - Allows to interface with Python to operate the FIB-SEMs

• Expert at SerialEM advanced scripting

• Expert in R

• Proficient in Python/numpy/Jupyter notebook scripting (interfacing with TFS Autoscript and SerialEM)

• Knowledge in Machine Learning, Pytorch and tensorflow (mainly using YOLO architecture for computer vision tasks)

Operation and regular alignment/troubleshooting of TEMs

• TFS Titan Krios + Falcon4i direct detector + Selectris energy filter

• TFS Talos Arctica + Falcon3 direct detector

Operation and regular alignment/troubleshooting of FIB-SEMs

• TFS Aquilos

• TFS Hydra (plasma-FIB)

Other lab manager duties

• Interfacing with service engineers

• Logging technical issues and their solutions

• Maintaining sample preparation equipment (glow-discharger, plunge freezers)

• Maintaining other miscellaneous equipment

• Ordering

• Consumable management and inventorying

• Training

• Performing experiments for users

Chemical fixation for electron microscopy

High Pressure Freezing (HPF)

• Baltec

• Leica EMPACT 2

Freeze Substitution (FS)

Plunge freezing

• Leica EM GP 2

• TFS Vitrobot

Microbiology

• liquid/solid cell culture

• G. hansenii cellulose biofilm culture

• on-EM grid culture

Botany

• liquid/solid cell culture

• Arabidopsis in-soil culture

• A. tumefaciens transient expression