Savvyscan software source files. Jan 2021. Editted/ written by Shahar Seifer, Elbaum lab, Weizmann Institute of Science, Israel.

Details in: Shahar Seifer, Lothar Houben, Michael Elbaum, "Flexible STEM with Simultaneous Phase and Depth Contrast", Microscopy and Microanalysis (2021), 27, 1476–1487.

Compilation and installation: The main project file is \ServerCamera\SERVER-SEMCamServer.vcxproj. Project can be built in VisualStudio community 2019 with full V142 platform toolset (including MFC), in 64 bits environment. Edit files \ServerCamera\BaseServer.cpp and \Spectrum\shahar\RecRepMulti.cpp to change the directory "d:\SavvyscanData" into which is your output data directory. Install SeiralEM interface using the settings suggested in directory Install_in_SerialEM. The system runs by starting the camera server, then the shadow GUI and SerialEM. Output file types: *.MRC and *.MAT. MAT files can be displayed with Matlab programs found in directory Post_Processing.

Version 2: Copy and overwrite the appropriate folders with the incremental project found in folder SavvyScan_version2.

The software has been extensively upgraded based on hundreds of hours of practice in cryo-STEM tasks.

• Supports OPAL detector as well as DECTRIS ARINA ultrafast camera for 4D-STEM.
• Spectrum cards run in FIFO mode, with latest firmware as for end of 2022.
• Spectrum cards synchronization is chosen either via STAR-HUB or cables.
• STEM camera extended to 8K x 8k pixels.
• Acquisition at highest sampling rate and digital averaging to improve signal sampling over integration time.
• Added scan patterns and improvement in existing ones. The raster scan is recommended for general purpose.
• Use of SerialEM python socket to temporary take control over serialEM and the microscope for special tasks, such as automated diffraction disc alignment of a quadrature detector.
• Full support of SeiralEM tilt series acquisition function. Scans longer than threshold time set in the GUI are considered record scans and stored in final MRC stack.
• Many bug fixes and robust performance.

Connection with LiberTEM-live software for live processing of DECTRIS pixelated detector data (see folder LiberTEM_server).