NDAABCDCCFOAINIAAADAAMP SCZHEALNBBPEC

Data Structure

Visium Image

Version 0110 Shared Subjects
Short Name: visiumimage01
Data Type: Genomics
Categories: Omics

Information to describe visium slide data in order to run spaceranger count software

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Definition
Submission Template

A Collection's submission must not be cumulative.

49 Elements

Name
Type
Required
Description
Value Range
Notes
subjectkeyGUIDRequiredThe NDAR Global Unique Identifier (GUID) for research subjectNDAR*
src_subject_idStringRequiredSubject ID how it's defined in lab/project
interview_dateDateRequiredDate on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_ageIntegerRequiredAge in months at the time of the interview/test/sampling/imaging.0::1440Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
sexStringRequiredSex of subject at birthM;F; O; NRM = Male; F = Female; O=Other; NR = Not reported
comments_miscStringRecommendedMiscellaneous comments on study, interview, methodology relevant to this form data
image_fileFileRecommendedData file (image, behavioral, anatomical, etc)
image_descriptionStringRecommendedImage description, i.e. DTI, fMRI, Fast SPGR, phantom, EEG, dynamic PET
scan_typeStringRecommendedType of ScanMR diffusion; fMRI; MR structural (MPRAGE); MR structural (T1); MR structural (PD); MR structural (FSPGR); MR structural (FISP); MR structural (T2); PET; ASL; microscopy; MR structural (PD, T2); MR structural (B0 map); MR structural (B1 map); single-shell DTI; multi-shell DTI; Field Map; X-Ray; static magnetic field B0; pCASL: ASL; MR: T2star; MR: FLAIR; Localizer scan; MR structural (FLASH); MR structural (MP2RAGE); MR structural (TSE); MR structural (T1, T2); 2D gradient echo; MR structural (MPnRAGE); Magnetic Resonance Spectroscopy(MRS); Neuromelanin MRI (NM-MRI); Functional Near Infrared Spectroscopy(fNIRS); MT; Magnetic Resonance Elastography (MRE); T1rho Spin-lock image; Image of Limb (IL); T2* Weighted Angiography (GE SWAN)
scan_objectStringRecommendedThe Object of the Scan (e.g. Live, Post-mortem, or PhantomLive; Post-mortem; Phantom
image_file_formatStringRecommendedImage file formatAFNI; ANALYZE; AVI; BIORAD; BMP; BRIK; BRUKER; CHESHIRE; COR; DICOM; DM3; FITS; GE GENESIS; GE SIGNA4X; GIF; HEAD; ICO; ICS; INTERFILE; JPEG; LSM; MAGNETOM VISION; MEDIVISION; MGH; MICRO CAT; MINC; MIPAV XML; MRC; NIFTI; NRRD; OSM; PCX; PIC; PICT; PNG; QT; RAW; SPM; STK; TIFF; TGA; TMG; XBM; XPM; PARREC; MINC HDF; LIFF; BFLOAT; SIEMENS TEXT; ZVI; JP2; MATLAB; VISTA; ecat6; ecat7; PAR/REC; FIF; NIRS; DAT; HEIC
data_file2FileRecommendeddata file 2
data_file2_typeStringRecommendeddata file 2 type/description
image_modalityStringRecommendedImage modalityMRI; PET; CT; SPECT; ultrasound; FA; X-Ray; spectroscopy; microscopy; DEXA; fNIRS; External Camera PhotographyComputed Radiography; Computed Tomography; External Camera Photography; FA; General Microscopy; MRI; Magnetic Resonance; Magnetic Resonance Spectroscopy; Nuclear Medicine; Single Photon Emission Computed Tomography; Ultrasound
transformation_performedStringRecommendedPerformed transformationYes; No
transformation_typeStringRecommendedType of transformation
image_historyStringRecommendedImage history,f.e. transformations steps and other modifications.
image_num_dimensionsIntegerRecommendedNumber of dimensions1 :: 5!=DICOM means not equal DICOM
image_extent1IntegerRecommendedExtent [1] X dimension1+!=DICOM means not equal DICOM
image_extent2IntegerRecommendedExtent [2] Y dimension1+
image_unit1StringRecommendedUnits [1] X dimensionInches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; frame number!=DICOM means not equal DICOM
image_unit2StringRecommendedUnits [2] Y dimensionInches; Centimeters; Angstroms; Nanometers; Micrometers; Millimeters; Meters; Kilometers; Miles; Nanoseconds; Microseconds; Milliseconds; Seconds; Minutes; Hours; Hertz; frame number
image_resolution1FloatRecommendedResolution [1] X dimension!=DICOM means not equal DICOM
image_resolution2FloatRecommendedResolution [2] Y dimension
objective_magnificationFloatRecommendedmagnification
objective_naFloatRecommendednumerical aperture of objective lens0.00::2.00
immersionIntegerRecommendedimmersion medium0::30=none; 1=oil; 2=water; 3=glycerol
exposure_timeFloatRecommendedexposure time in seconds
stainStringRecommendedStain used
stain_detailsStringRecommendedCritical details of stainingi method, e.g. source and dilution of antibody for immunohistochemistry.
pipeline_stageIntegerRecommendedStage of image in processing pipeline.1::31 = original; 2 = intermediate; 3 = final
deconvolvedIntegerRecommendedWas deconvolution used to obtain the image?0::20 = no; 1 = yes; 2 = unknown
decon_softwareStringRecommendeddeconvolution software
decon_methodStringRecommendedMethod of deconvolution.
psf_typeStringRecommendedType of point spread function used for deconvolutionE; TE = empirical; T = theoretical
psf_fileStringRecommendedName of empirical point spread function file.
decon_snrFloatRecommendedSignal to noise ratio used for deconvolution
decon_iterationsIntegerRecommendedNumber of iterations used for deconvolution
micro_temmplate_nameStringRecommendedName of microscope template used for deconvolution
in_stackIntegerRecommended2D image is part of 3D stack0;10 = no; 1 = yes
decon_template_nameStringRecommendedName of deconvolution template used for deconvolution.
stackStringRecommendedName of stack
slicesIntegerRecommendedNumber of images in entire stack2::2000
slice_numberIntegerRecommendedSequence in stack1::2000
slice_thicknessFloatRecommendedspacing between image planes, in microns
type_of_microscopyStringRecommendedtype of microscopyBF; WFF; CFF; 2Pbright field, wide field fluorescensce, confocal fluorescensce, 2-photon
excitation_wavelengthIntegerRecommendedexcitation wavelength in nanometers100::1200
manifestManifestRecommended
emission_wavelengthStringRecommendedemission wavelength in nanometers100-1200