List of custom descriptors for user-defined key-value pairs describing how movies were obtained or any related information
Cryo electron tomography dataset of an environmental sample
List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
A series of numbers constructed from min, max, and increment
Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
Unifying class to describe the full sample.
Instrument values, mostly constant across a data collection.
Overarching category for authors and grants
General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
Special device used to correct instrument inherent chromatic aberration.
A device used to filter for electrons with specific energy.
Used to modulate the phase of the electron wave.
Optional optics used to correct for instrument limitations.
Special device used to correct instrument inherent spherical aberration.
Usually used for larger organic complexes, such as organoids or even tissue samples.
Typically used for smaller and thinner samples in both SPA and tomography.
base information on the acquisition and treatment of the sample itself.
how the frozen sample was thinned by i.e. FiB-milling
what was the target of the tomograms, and what area of a cell do they cover.
the organism(s) present in your sample, if not perfectly defined try to asses as close as possible.
Details on the person performing the experiment.
List of authors associated with the project
List of grants associated with the project
The min, max and increment of the tilt angle in a tomography session. Unit is degree.
Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
Level of binning on the images applied during data collection
Machine estimated defocus, min and max values in µm. Has a tendency to be off.
Specialist device to correct for chromatic aberration of the microscope lenses
Collection angle set, min and max values in mrad.
Cryogen used in cooling the instrument and sample, usually nitrogen
Dispersion of an analytical detector, in eV
Average dose per image/movie/tilt - given in electrons per square Angstrom
Whether an energy filter was used and its specifics.
Time of data acquisition per movie/tilt - in s
Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
Whether and how you have to flip or rotate the gainref in order to align with your acquired images
Number of grids imaged for this project - here with qualifier during this data acquisition
Type of cryogen used in the holder - if the holder is cooled seperately
The size of the image in pixels, height and width given.
Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
Target defocus set, min and max values in nm.
Magnification level as indicated by the instrument, no unit
Phaseplate is a special optics device that can be used to enhance contrast
The total electron beam current hitting the viewing screen, in nA.
Any type of special optics, such as a phaseplate
Specialist device to correct for spherical aberration of the microscope lenses
Specifies which Acquisition subschema/class is in use.
Temperature during data collection, in K with min and max values.
if a value has a unit, it should be given as a unit value pair.
The height of a given item - unit depends on item
Maximal value of a given dataset property
Minimal value of a given dataset property
value of a given field in respect to its SI unit
The width of a given item - unit depends on item
What was the atmosphere the sample was in right before freezing, elaborate on any special gases present etc.
What type of cellular features are present in your tomograms?
the cryogen used to freeze the sample, i.e. ethane
Any further comments on the freezing process go here.
If you have any further comments on your tomograms please leave them here
What was done to the sample, please give an overview of relevant treatments.
humidity of the atmosphere right before/ during freezing; in %.
the geographical location of your source, optimally in a geographic coordinate system.
What was the main biological target of your research for this tomogram?
freezing method - such as plunge freezing, high pressure freezing etc.
The thinning method used, such as FIB milling.
where is this sample from? i.e. Hospital
What was the target thickness of the lamella; in nm.
temperature of the sample right before freezing; in K.
if the sample is a tissue sample please indicate what type of tissue.
Voltage used for the electron acceleration, in kV
Refers to how tightly or widely the electron beam is focused onto the sample, in mrad. Typically low convergence for TEM and high for STEM.
C2 aperture size used in data acquisition, in µm
Spherical aberration of the instrument, in mm
Type of electron source used in the microscope, such as FEG
Mode of illumination used during data collection
Mode of imaging used during data collection
Operating mode of the microscope, i.e. "TEM", "STEM"
ORCID of the author, a type of unique identifier
Role of the author, for example principal investigator
The tilt axis angle of a tomography series
an axis-aligned 2D bounding box (float units)
Type of organization, academic, commercial, governmental, etc.
Details of a given specialist instrument
Any type, used as the base for type-narrowing.
Allowed values for authors organizations.
whether a specific instrument was used during data acquisition
unit value extended to have two additional fields si_value and si_unit