Image Metadata Glossary
Following is a glossary of the metadata fields available for inclusion in converted image files using Microfile+ software. The fields and their definitions are from the OME TIFF specification.
The asterisk symbol * indicates a required metadata field that must be filled out before conversion if the option Require metadata entry before saving is selected in the Save Format window.
Channel
The Channel section includes information about each separate channel in the image. There must be one per channel in the Image, even for a single-plane image. The channel section collects/adds metadata for the modality, pseudocolor, emission filter, excitation filter, exposure, target fluorophore used, channel ID, neutral density filter, and target label for each channel.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| Modality | Describes the type of microscopy performed for each channel. |
Image / Pixels / Channel / AcquisitionMode |
| Pseudocolor | A color used to render this channel - encoded as RGBA. |
Image / Pixels / Channel / Color |
| Emission Filter | Wavelength of emission for a particular channel. |
Image / Pixels / Channel / EmissionWavelength |
| Excitation Filter | Wavelength of excitation for a particular channel. |
Image / Pixels / Channel / ExcitationWavelength |
| Exposure | The length of the exposure. |
Image / Pixels / Plane / ExposureTime |
| Target Fluorophore | The name of the fluorophore used to produce this channel. |
Image / Pixels / Channel / Fluor |
| ID | Channel unique identifier. |
Image / Pixels / Channel / ID |
| Neutral Density Filter | Specifies the combined effect of any neutral density filters used. |
Image / Pixels / Channel / NDFilter |
| * Target Label | A name for the channel that is suitable for presentation to the user. |
Image / Pixels / Channel / Name |
Detector (Camera)
The Detector (or camera) section describes the detector used to capture the image. The detector section collects/adds metadata for the ID, model, name, and type of the detector/camera.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| ID | Camera unique identifier | Instrument / Detector / ID |
| Model | The model of the component | Instrument / Detector / Model |
| Name | The manufacturer of the component | Instrument / Detector / Manufacturer |
| Type | The type of detector, e.g., CCD, PMT, EMCCD, etc. | Instrument / Detector / Type |
Device
Describes the instrument used to capture the Image. The device section collects/adds metadata for the ID, model, name, and type of the device.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| ID | Device unique identifier | Instrument / ID |
| Model | The Model of the component | Instrument / Microscope / Model |
| Name | The manufacturer of the component | Instrument / Microscope / Manufacturer |
| Type | The Type of device | Instrument / Microscope / Type |
Image
The image section describes the image and its metadata. It collects/adds metadata for the bits per pixel, image name, originX, originY, originZ, number of channels, pixels in X, pixels in Y, and number of Z planes.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| * BitsPerPixelUsed | The number of bits within the type storing each pixel that are significant | Image / Pixels / SignificantBits |
| * Name | Filename; default is to use the file the ome-xml data has been pulled from | Image / Pixels / TiffData / UUID / FileName |
| OriginX | Defines the X position to use for the origin of the fields (individual images) taken in a well | Plate / WellOriginX |
| OriginY | Defines the Y position to use for the origin of the fields (individual images) taken in a well | Plate / WellOriginY |
| OriginZ | Defines the Z position to use for the origin of the fields (individual images) taken in a well | Plate / WellOriginZ |
| SizeC | Dimensional size of pixel data array in the c direction (number of channels) | Image / Pixels / SizeC |
| * SizeX* | Dimensional size of pixel data array in the x direction. | Image / Pixels / SizeX |
| * SizeY | Dimensional size of pixel data array in the y direction | Image / Pixels / SizeY |
| * SizeZ | Dimensional size of pixel data array in the z direction | Image / Pixels / SizeZ |
Info
The information section includes additional information about the image and collects/adds metadata for the date created, miscellaneous notes, name of experiment preset used, number of images included, post processing measures, the software used, filenames of all files used in conversion, X scaling, Y scaling, Z scaling, and the universally unique identifier (UUID).
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| * DateCreated | The acquisition date of the Image OR the conversion date. This field may vary between either date. | |
| Misc | Comments regarding the image | |
| * Name | Filename; default is to use the filename the ome-xml data has been pulled from | Image / Pixels / TiffData / UUID / FileName |
| * NumImages | The number of images contained in the file | |
|
PostProcessing |
Post-processing measures taken with the image, i.e. histogram max, min, gamma, etc. |
|
| * Software | The name of the creating application of the OME-XML and its full version |
OME / Creator |
| SourceFiles | The names of all original images used in conversion/combination |
|
| * SpacingX | Physical size of a pixel in the x direction | Image / Pixels / PhysicalSizeX |
| * SpacingY | Physical size of a pixel in the y direction | Image / Pixels / PhysicalSizeY |
| SpacingZ | Physical size of a pixel in the z direction | Image / Pixels / PhysicalSizeZ |
| UUID | The unique identifier of another OME-XML block whose metadata describes the binary data in this file |
OME / BinaryOnly |
Objective
The objective section describes the microscope's objective lens and collects/adds metadata for the ID, immersion media, numerical aperture, magnification, model, refractive index, and make of the objective used.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| ID | Objective unique identifier | Instrument / Objective / ID |
| Immersion | The immersion medium the lens is designed for | Instrument / Objective / Immersion |
| LensNA | The numerical aperture of the lens expressed as a floating point (real) number; expected range 0.02 - 1.5 | Instrument / Objective / LensNA |
| Magnification | The magnification of the objective | Instrument / Objective / CalibratedMagnification |
| Model | The Model of the component | Instrument / Objective / Model |
| RefractiveIndex | (Refractive Index): The immersion medium; this is a ratio so it is unit-less. | Instrument / ObjectiveSettings / RefractiveIndex |
| Make | The manufacturer of the component | Instrument / Objective / Manufacturer |
PMT
The PMT section describes the photomultiplier tube and collects/adds metadata for the manufacturer and model of the photomultiplier tube used.
|
Field |
Description |
Position in the OME Tiff specification |
|---|---|---|
| Model | The Model of the component | Instrument / Detector / Model |
| Manufacturer | The manufacturer of the component | Instrument / Detector / Manufacturer |
Additionally, the Compression Type and Level will be written to JPEG2000 files that are compressed.
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