4d — Microscope

Microscope — the instrument these data come from

The Microscope page of Preferences describes the electron microscope this installation of 4d works with: its name, and the optical constants that every processing step needs but that the image files do not always carry. The values live in the user-level configuration file 4d.cfg and apply to every project you open on this computer.

The ? button at the right end of the Microscope Parameters title line opens this page.

Screenshot images/screenshot-preferences-microscope.png not found — place it in the manual’s images/ directory.

Each row shows the parameter’s label and its current value. Edit the value in place; when you leave the field it is written to your user configuration if Automatically save configurations when they are changed (General) is on, and otherwise kept in memory until you save explicitly. Hover a label to see the parameter’s explanation (the LEGEND text of the entry).

Microscope Parameters

These four entries are the defaults of the instrument. They matter most at import: when a recording arrives without the corresponding value in its header or metadata file, the processing scripts fall back to what is set here. A value already known for an image is never overwritten by these defaults, so correcting a wrongly detected voltage on a single image stays in effect.

Parameter	Label	Meaning	Default
`Microscope_Name`	Microscope or System Name	A name for this microscope or computer system. It identifies the instrument in the subject and header of the status e-mails 4d sends, so give each microscope of a facility its own name.	`CryoEM`
`Default_CS`	Default Microscope CS	Spherical aberration constant C_s of the objective lens, in millimetres. It enters every CTF fit; a wrong value biases the fitted defocus. Typical values are 2.7 mm for an uncorrected Titan/Glacios and 0.01 mm for a C_s-corrected instrument.	2.7
`Default_KV`	Default Microscope High Tension [kV]	Acceleration voltage of the microscope, in kilovolts — 300, 200 or 120 kV for most instruments. It sets the electron wavelength used by the CTF fit and by every resolution estimate.	300.0
`Default_phase_shift_doit`	Default PhasePlate setting: Do you have a phase plate?	`y` when the microscope has a phase plate, so that the CTF fit searches for an additional phase shift by default; `n` otherwise. Searching for a phase shift that is not there costs time and can destabilise the fit.	`n`

The C_s, voltage and phase-plate settings are consumed by the processing scripts (CTF estimation with CTFFIND/Gctf, drift correction, Relion classification, and the import scripts). Changing them here affects recordings processed from then on; images already processed keep the values stored with them until they are reprocessed.

Working with two microscopes from one computer? Set the values of the instrument you use most here, and correct the exceptions per project in Parameters or per image in the Library — project and image values take precedence over these defaults.