The controlled terms related to this schema need to be validated. See the table below.
| Field |
controlled terms |
scanPattern |
raster, spiral, randomAccess, lightSheetPlane |
scanningMode |
resonant, galvo, rollingShutter, global |
imagingMode |
epifluorescence (a.k.a. one-photon, widefield), confocal (point scanning), spinningDiskConfocal, twoPhoton (2P), threePhoton (3P),lightSheet (SPIM) |
NB: OphysAcquisition schema:
| Field |
Description |
Required |
type |
imagingMode |
The optical imaging modality used during acquisition |
Yes |
controlled term |
scanPattern |
Pattern used by the scanner to traverse the sample (e.g., raster, spiral, randomAccess, lightSheetPlane). |
Optional |
controlled term |
scanningMode |
Scanner mechanism or readout type |
Optional |
controlled term |
| --------------- |
---------------------------------------------------- |
-------- |
---- |
setup |
Add the setup used for this |
Yes |
linked -> OphysSetup |
zoomFactor |
Dimensionless zoom setting applied in the microscope optics (affects FOV and pixel size). |
Optional |
number (dimensionless) |
frameRate |
Imaging frame rate, expressed as the number of frames acquired per second. |
Yes |
QuantitativeValue |
fieldOfView |
The spatial extent of the imaged region in micrometers (width, height, optional depth). |
Yes |
linkedCategories -> mathematicalShapes |
pixelSize |
Effective sampling size of each pixel along x, y (and optional z) dimensions, in micrometers. |
Yes |
QuantitativeValueArray |
numberOfPlanes |
Number of imaging planes acquired in the session (for multiplane or volumetric imaging). |
Optional |
integer |
planeSeparation |
Distance between successive imaging planes, in micrometers. |
Optional |
QuantitativeValue |
filterWheelPositions |
Filters or emission bands selected during the acquisition (e.g., 525/50 nm, 605/70 nm). |
Optional |
array of strings (wavelength bands) |
The controlled terms related to this schema need to be validated. See the table below.
scanPatternscanningModeimagingModeNB: OphysAcquisition schema:
imagingModecontrolled termscanPatterncontrolled termscanningModecontrolled termsetupOphysSetupzoomFactorframeRateQuantitativeValuefieldOfViewmathematicalShapespixelSizeQuantitativeValueArraynumberOfPlanesplaneSeparationQuantitativeValuefilterWheelPositions