Attribute Manifest Name Description Required Conditional If Data Type Valid Values Filename Imaging Level 1,Imaging Level 2,Imaging Level 3 Segmentation,Imaging Level 4 Name of a file True String File Format Imaging Level 1,Imaging Level 2,Imaging Level 3 Segmentation,Imaging Level 4 Format of a file (e.g. txt, csv, fastq, bam, etc.) True String hdf5 bedgraph idx idat bam bai excel powerpoint tif tiff OME-TIFF png doc pdf fasta fastq sam vcf bcf maf bed chp cel sif tsv csv txt plink bigwig wiggle gct bgzip zip seg html mov hyperlink svs Md flagstat gtf raw msf rmd bed narrowPeak bed broadPeak bed gappedPeak avi pzfx fig xml tar R script abf bpm dat jpg locs Sentrix descriptor file Python script sav gzip sdf RData hic ab1 7z gff3 json sqlite svg sra recal tranches mtx tagAlign dup DICOM czi mex cloupe Am cell am mpg M mzML scn dcc rcc pkc sf bedpe HTAN Parent Biospecimen ID Imaging Level 1,Imaging Level 2 HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated True Is lowest level is "Yes - Is lowest level" String HTAN Data File ID Imaging Level 1,Imaging Level 2,Imaging Level 3 Segmentation,Imaging Level 4 Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz) True String Imaging Assay Type Imaging Level 1,Imaging Level 2 Type of imaging assay True String H&E CyCIF t-CyCIF IHC mIHC MxIF SABER IMC CODEX GeoMX-DSP MIBI MERFISH ExSeq RareCyte Orion Not Applicable Protocol Link Imaging Level 1,Imaging Level 2 Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. True String Software and Version Imaging Level 1,Imaging Level 2,Imaging Level 3 Segmentation,Imaging Level 4 Name of software used to generate expression values. String True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String Commit SHA Imaging Level 1,Imaging Level 3 Segmentation,Imaging Level 4 Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple] False String Pre-processing Completed Imaging Level 1 Pre-processing steps completed to convert level 1 raw data to a single level 2 image True String Illumination correction Tile Stitching Channel/Cycle Registration TMA de-arraying None Other Pre-processing Required Imaging Level 1 Pre-processing steps required to convert level 1 raw data to a single level 2 image True String Illumination correction Tile Stitching Channel/Cycle Registration TMA de-arraying None Other Comment Imaging Level 1,Imaging Level 2 Free text field (generally for QC comment) False Passed QC is "No - Channels QC" String HTAN Participant ID Imaging Level 2 HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ) True String Channel Metadata Filename Imaging Level 2 Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details True String Microscope Imaging Level 2 Microscope type (manufacturer, model, etc) used for this experiment True String Objective Imaging Level 2 Objective False String NominalMagnification Imaging Level 2 The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) True String LensNA Imaging Level 2 The numerical aperture of the lens. Floating point value > 0. False String WorkingDistance Imaging Level 2 The working distance of the lens, expressed as a floating point number. Floating point > 0. False String WorkingDistanceUnit Imaging Level 2 The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) False String cm mm µm nm Å Immersion Imaging Level 2 Immersion medium False String Air Oil Water Other Pyramid Imaging Level 2 Does data file contain pyramid of images True String yes no Zstack Imaging Level 2 Does data file contain a Z-stack of images True String yes no Tseries Imaging Level 2 Does data file contain a time-series of images True String yes no Passed QC Imaging Level 2 Did all channels pass QC (if not add free text Comment) True String yes No - Channels QC FOV number Imaging Level 2 Index of FOV (as it pertains to its sequence order). Integer >= 1 False String FOVX Imaging Level 2 Field of view X dimension. Floating point False String FOVXUnit Imaging Level 2 Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) False String cm mm µm nm Å FOVY Imaging Level 2 Field of view Y dimension. Floating point value False String FOVYUnit Imaging Level 2 Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) False String cm mm µm nm Å Frame Averaging Imaging Level 2 Number of frames averaged together (if no averaging, set to 1). Integer >= 1 False String Image ID Imaging Level 2 Unique internal image identifier. eg "Image:0". (To be extracted from OME-XML) True String DimensionOrder Imaging Level 2 The order in which the individual planes of data are interleaved. True String XYZCT XYZTC XYCTZ XYCZT XYTZC ZYX PhysicalSizeX Imaging Level 2 Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0. True String PhysicalSizeXUnit Imaging Level 2 The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) True String cm mm µm nm Å PhysicalSizeY Imaging Level 2 Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0. True String PhysicalSizeYUnit Imaging Level 2 The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) True String cm mm µm nm Å PhysicalSizeZ Imaging Level 2 Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0. True String PhysicalSizeZUnit Imaging Level 2 The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) True String cm mm µm nm Å Pixels BigEndian Imaging Level 2 Boolean (True/False) True String true false PlaneCount Imaging Level 2 Number of Z-planes (not to be confused with downsampled "pyramid"). Integer >=1 True String SizeC Imaging Level 2 Number of channels. Integer >= 1 True String SizeT Imaging Level 2 Number of time points. Integer >= 1 True String SizeX Imaging Level 2 Size of image: X dimension (in pixels). Integer >= 1 True String SizeY Imaging Level 2 Size of image: Y dimension (in pixels). Integer >= 1 True String SizeZ Imaging Level 2 Size of image: Z dimension (in pixels). Integer >= 1 True String PixelType Imaging Level 2 Data type for each pixel value. E.g. "uint16" True String int8 int16 int32 uint8 uint16 uint32 float double bit MERFISH Positions File Imaging Level 2 The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay. False String MERFISH Codebook File Imaging Level 2 The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name. False String HTAN Parent Data File ID Imaging Level 3 Segmentation,Imaging Level 4 HTAN Data File Identifier indicating the file(s) from which these files were derived True String Imaging Segmentation Data Type Imaging Level 3 Segmentation Specifies how the segmentation is stored True String Mask Outline Polygon Probability Map Point Parameter file Imaging Level 3 Segmentation,Imaging Level 4 Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis False String Imaging Object Class Imaging Level 3 Segmentation,Imaging Level 4 Defines the structure that the mask delineates True String nucleus cytoplasm plasma membrane whole cell spot Imaging Object Class Other Number of Objects Imaging Level 3 Segmentation,Imaging Level 4 The number of objects (eg cells) described True String HTAN Parent Channel Metadata ID Imaging Level 4 HTAN ID for a level 3 channels table. True String Number of Features Imaging Level 4 The number of features (eg channels) described True String Imaging Summary Statistic Imaging Level 4 Function used to summarize object/feature intensity False String Mean Median Not Specified No - Channels QC Imaging Level 2 Not all channels passed QC False String Imaging Object Class Other Imaging Level 3 Segmentation Imaging Object Class Other False String Imaging Object Class Description Imaging Level 3 Segmentation Free text description of object class [string] True Imaging Object Class is "Imaging Object Class Other" String