Common Imaging Fields

	A	B	C	D	E
1	This is a list of XML fields required in the XML header of HuBMAP and SenNet OME TIFF files. All of the fields listed here should reside within either the Pixels block in the XML header.
2	This is not a comprehensive list of all fields to be included in the XML header. Rather data providers should aim to include as much additional information as feasible in the XML header.
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4	Bio Formats can be used to read/write the XML header. If users have questions about what to include in the OME TIFF XML header or how to use Bio Formats, please email the Help Desk.
5	Details about the OME data model		HuBMAP Help Desk
6	Bio Formats download and documentation		Example OME-TIFF XML Header
7	Bio Formats Cheat Sheet		Spatialdata-io is another conversion platform to consider

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9	OME Data Model and File Format Version:		6.0.1
10	Field Name	Data type	Definition	Example	Notes
11	Field Name	Data type	Definition	Example	Notes
12	Pixels_DimensionOrder	categorical	This field records the order in which the individual planes of data are interleaved in the Image. [Values: XYZCT, XYZTC, XYCTZ, XYCZT, XYTCZ, XYTZC]	XYCZT
13	Pixels_Type	categorical	This field records the data type used to represent the Pixel Intensity in the Image. [Values: bit, complex, double, double-complex, float, int8, int12, int14, int16, int32, uint8, uint12, uint14, uint16, uint32, Other]	uint8
14	Pixels_SizeX	integer	X size of pixel data array	20245
15	Pixels_SizeY	integer	Y size of pixel data array	20703
16	Pixels_SizeZ	integer	Number of Z-planes	1
17	Pixels_SizeC	integer	Number of Channels used in this Image	3
18	Pixels_SizeT	integer	This field records the number of Timepoints used in this Image.	1
19	Pixels_PhysicalSizeX	float	Physical width of a pixel in the image. This should include the magnification factors, so the OME-XML allows someone to determine what physical area is captured by each pixel.	0.454	Multiplying this physical size by the number of pixels in the X dimension (e.g., 20,000) should give values on the order of the physical dimension of a Visium capture slide, plus any border area captured by the image (so values between 8mm and 10mm are appropriate). pixel physical size (in μm) = (physical size of the pixel in the CCD/EMCCD camera) / (total magnification in the image) total magnification in the image = (objective magnification) + (any other sources of magnification) Note, the most common source of extra magnification would be the camera mount adapter. For example, a Visium experiment used a 10x objective with a CCD camera that had a physical detection unit width (typically the X dimension) of 4.54um, as reported in the corresponding PixelWidth field in the microscope_hardware.json file. Starting from the physical size of the detection unit, it is possible to derive the physical dimension each pixel represents in the image. To this aim, the Pixel Physical Size is computed as (physical pixel width in the camera chip / total magnification) and should be reported in the OME-TIFF header as PhysicalPixelSizeX. In our example here, this works out to a PhysicalSizeX of (4.54 / 10) = 0.454um. The example OME-TIFF image has 20,245 pixels in the X dimension. Using the computed PhysicalSizeX, we can compute the physical width of the image as (physical pixel size * total pixels). In our example this is (0.454um * 20,245) = 9,191um or 9.191mm. We know the Visium fiducial frame is 8mm wide, so our numbers appear internally consistent.
20	Pixels_PhysicalSizeXUnit	categorical	default µm	µm
21	Pixels_PhysicalSizeY	float	Physical height of a pixel in the image. This should include the magnification factors, so the OME-XML allows someone to determine what physical area is captured by each pixel.	0.454	Multiplying this physical size by the number of pixels in the Y dimension (e.g., 20,000) should give values on the order of the physical dimension of a Visium capture slide, plus any border area captured by the image (so values between 8mm and 10mm are appropriate). pixel physical size (in μm) = (physical size of the pixel in the CCD/EMCCD camera) / (total magnification in the image) total magnification in the image = (objective magnification) + (any other sources of magnification) Note, the most common source of extra magnification would be the camera mount adapter. For example, a Visium experiment used a 10x objective with a CCD camera that had a physical detection unit height (typically the Y dimension) of 4.54um, as reported in the corresponding PixelHeight field in the microscope_hardware.json file. Starting from the physical size of the detection unit, it is possible to derive the physical dimension each pixel represents in the image. To this aim, the Pixel Physical Size is computed as (physical pixel height in the camera chip / total magnification) and should be reported in the OME-TIFF header as PhysicalPixelSizeY. In our example here, this works out to a PhysicalSizeY of (4.54 / 10) = 0.454um. The example OME-TIFF image has 20,703 pixels in the Y dimension. Using the computed PhysicalSizeY, we can compute the physical height of the image as (physical pixel size * total pixels). In our example this is (0.454um * 20,703) = 9,399um or 9.399mm. We know the Visium fiducial frame is 8mm wide, so our numbers appear internally consistent.
22	Pixels_PhysicalSizeYUnit	categorical	default µm	µm
23	Pixels_PhysicalSizeZ	float	Physical distance between optical planes. If the image is 2D then this value should be the thickness of the slice.	0.01
24	Pixels_PhysicalSizeZUnit	categorical	default µm	µm
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