Clinical_Imaging_Metadata_Specification.xlsx

	A	B	C	D	E	F	G	H	I	J	K	L	M	N
1	Columns B through G can go to Chuck McCallum for publication of this metadata schema in Github	Total. fieldnames in red will be new fields for HuBMAP metadata.	descriptions	Required - T or F	input type	constrained input?	enums	MicroCT	OCT	Ultrasound	MRI	body CT	examples?	NOTES

2		donor_id		T				donor_id	donor_id	donor_id	donor id	donor id
3		tissue_id		T				tissue_id	tissue_id	tissue_id	tissue id	tissue id
4		execution_datetime		T				execution_datetime	execution_datetime	execution_datetime	execution datetime	execution datetime
5		protocols_io_doi		T				protocols_io_doi	protocols_io_doi	protocols_io_doi	protocols io doi
6		operator		T				operator	operator	operator	operator
7		operator_email		T				operator_email	operator_email	operator_email	operator email
8		pi		T				pi	pi	pi	pi	pi
9		pi_email		T				pi_email	pi_email	pi_email	pi email	pi email
10		assay_category		T				assay_category	assay_category	assay_category	assay category	assay category
11		assay_type		T				assay_type	assay_type	assay_type	assay type	assay type
12		acquisition_instrument_vendor		T				acquisition_instrument_vendor	acquisition_instrument_vendor	acquisition_instrument_vendor	acquisition instrument vendor	acquisition instrument vendor
13		acquisition_instrument_model		T				acquisition_instrument_model	acquisition_instrument_model	acquisition_instrument_model	acquisition instrument model	acquisition instrument model
14		contributors_path		T				contributors path	contributors path	contributors path	contributors path	contributors path
15		data_path		T				data path	data path	data path	data path	data path
16		single_file_export_format	The format in which each single imaging file will be exported (Example: DICOM, tiff, avi, etc)	T	string	no		single file export format	single file export format	single file export format	single file export format	single file export format
17		max_x_width_value	Image width value of the ROI acquisition	T	float	no		max x width value	max x width value	max x width value	max x width value	max x width value
18		max_x_width_unit	Units of image width of the ROI acquisition	T		yes	um, mm	max x width unit	max x width unit	max x width unit	max x width unit	max x width unit
19		max_y_height_value	Image height value of the ROI acquisition	T	float	no		max y height value	max y height value	max y height value	max y height value	max y height value
20		max_y_height_unit	Units of image height of the ROI acquisition	T	string	yes	um, mm	max y height unit	max y height unit	max y height unit	max y height unit	max y height unit
21		roi_description	A description of the region of interest (ROI) captured in the image.	T		no		roi description	roi description	roi description	roi description	roi description
22		roi_id	Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide.	F	integer	no		roi_id	roi_id	roi_id	-	-
23		resolution_x_value	The width of a pixel.	T	float	no		resolution x value	resolution x value	resolution x value	resolution x value	resolution x value
24		resolution_x_unit	The unit of measurement of the width of a pixel.	T		yes	nm, um, mm	resolution x unit	resolution x unit	resolution x unit	resolution x unit	resolution x unit
25		resolution_y_value	The height of a pixel	T		no		resolution y value	resolution y value	resolution y value	resolution y value	resolution y value
26		resolution_y_unit	The unit of measurement of the height of a pixel.	T		yes	nm, um, mm	resolution y unit	resolution y unit	resolution y unit	resolution y unit	resolution y unit
27		resolution_z_value	Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes.	F		no		resolution z value	resolution z value	??	resolution z value	resolution z value
28		resolution_z_unit	The unit of incremental distance between image slices.(um)	F		yes	nm, um, mm	resolution z unit	resolution z unit	??	resolution z unit	resolution z unit
29		pixel_size_z_value	Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value).	F		no		pixel size z value	pixel size z value	??	pixel size z value
30		pixel_size_z_unit	Depth unit of the pixel or voxel measurement.	F		yes	nm, um, mm	pixel size z unit	pixel size z unit	??	pixel size z unit
31		number_of_images	The total number of images in the dataset.	T	integer	no		number of images	number of images	-	number of images	number of images
32		voltage_value	The voltage used to acquire images	F	float	no		voltage_value
33		voltage_unit	The unit of the voltage used to acquire microCT images. Example: volt	F	string	yes	Volts (V), kV	voltage_unit
34		current_value	The current used to acquire microCT images	F	float	no		current_value
35		current_unit	The unit of the current used to acquire microCT images. Example: amp	F	string	yes	mAmp, microAmp, Amp	current_unit
36		filter	The filter used to acquire microCT images	F	string	no		filter
37		imaging_threshold_value	The threshold used for analyzing microCT images	F	float	no		imaging_threshold_value
38		imaging_threshold_unit	The threshold unit used for analyzing microCT images (unitless)	F	integer or float?			imaging_threshold_unit
39		total_sections_analyzed	The number of sections used for analyzing microCT or OCT images	F	integer	no		total sections analyzed	total_sections_analyzed
40		wavelength_value	The value of the wavelength used to acquire OCT images (Example: 787)	F	float	no			wavelength_value
41		wavelength_unit	The unit of the wavelength value used to acquire OCT images (nm)	F	string	yes	nm		wavelength_unit
42		volume_export_format	The format of the volume export of OCT images (Example: tiff)	F	string	yes	tiff, avi		volume_export_format
43		sn_quality	An integer describing the signal to noise quality of an OCT image (Example: 30)	F	float	no			sn_quality
44		sn_quality_unit	The unit of the integer describing the signal to noise quality of an OCT image (Example: dB)	F	string	yes	dB		sn_quality_unit
45		quality_view	The quality of the acquired ultrasound images.	F	string	yes	high confidence/optimal, low confidence/sub-optimal, no confidence			quality_view
46		probe	The specific ultrasound device used to produce sound waves (String -free text). Examples: C1-5-D, C4-8-D, AB2-7-D, RIC5-9-D, RAB6-D, RAB4-8-D, 4C-D, RM6C	F	string	no				probe
47		dynamic_contrast	Level of echo intensity on an ultrasound. Examples: none (blank) or 1-10.	F	integer	no				dynamic_contrast
48		speckle_reduction_imaging	Level used to reduce speckle noise in ultrasound images. Examples: numbers ranging from 0-5	F	integer	no	0, 1, 2, 3, 4, 5			speckle_reduction_imaging
49		compound_imaging	Level used to increase image resolution in ultrasounds by using multiple lines of site to eliminate artifacts, shadows, and increase edge detail (aka crossbeam). Examples: Either none or 0-5	F	integer	no				compound_imaging
50		harmonics	Multiples of the fundamental or transmitted frequency used to help optimize an ultrasound image. Examples: None, Low, Medium or High	F	string	no	None, Low, Medium or High			harmonics
51		frequency	Frequency at which the imaging device is operating.	F	float	no				frequency	frequency
52		frequency_unit	Unit of frequency at which the imaging device is operating. Example: Hz, kHz, MHz	F	string	Yes	Hz, kHz, MHz			frequency_unit	frequency_unit
53		coil	Receiver coil name used to collect MRI data. Example: 32 channel body coil	F	string	no					coil
54		field_strength_value	MRI scanner magnetic field strength value	F	float	no					field_strength
55		field_strength_unit	MRI scanner magnetic field strength in units of Tesla [T]	F	string	yes	Tesla
56		scanning_sequence	Pulse sequence used to collect MRI data	F	string	no	spin echo, inversion recovery, gradient echo, echo planar, research mode,				scanning_sequence
57		sequence_variant	Variant of the Scanning Sequence	F	string	no	segmented k-space, magnetization transfer contrast, steady state, time reversed steady state, spoiled , magnetization prepared, oversampling phase, no sequence variant				sequence_variant
58		echo_time_(TE)	Time in msec between the middle of the excitation pulse and the peak of the echo produced (kx=0). In the case of segmented k-space, the TE(eff) is the time between the middle of the excitation pulse to the peak of the echo that is used to cover the center of k-space (i.e., -kx=0, ky=0).	F	float	no					echo_time_(TE)
59		repetition_time_(TR)	The period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence.	F	float	no					repetition_time_(TR)
60		flip_angle	Steady state angle in degrees to which the magnetic vector is flipped from the magnetic vector of the primary field.	F	integer	no					flip_angle
61		echo_train_length_(ETL)	Number of lines in k-space acquired per excitation per image.	F	integer	no					echo_train_length_(ETL)
62		acquisition_matrix_size_in_frequency_encoding_direction	Dimensions of the acquired frequency data before reconstruction.	F	integer	no					acquisition_matrix_size_in_frequency_encoding_direction
63		acquisition_matrix_size_in_phase_encoding_direction	Dimensions of the acquired phase data before reconstruction, per image.	F	integer	no					acquisition_matrix_size_in_phase_encoding_direction
64		number_of_image_rows	Number of rows of the reconstructed data, per image.	F	integer	no					number_of_image_rows
65		number_of_image_columns	Number of columns of the reconstructed data.	F	integer	no					number_of_image_columns
66		number_of_averages	Number of times a given pulse sequence is repeated in the collection of a single image or volume.	F	float	no					number_of_averages
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