Attribute Manifest Name Description Required Conditional If Data Type Valid Values Filename Electron Microscopy Level 1,Electron Microscopy Level 2,Electron Microscopy Level 3,Electron Microscopy Level 4 Name of a file True String File Format Electron Microscopy Level 1,Electron Microscopy Level 2,Electron Microscopy Level 3,Electron Microscopy 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 Electron Microscopy Level 1 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 Electron Microscopy Level 1,Electron Microscopy Level 2,Electron Microscopy Level 3,Electron Microscopy Level 4 Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz) True String EM method Electron Microscopy Level 1 Electron microscopy method used True String SEM FIB-SEM SBF-SEM AT TEM ET cryo ET ssTEM EM signal or contrast mech Electron Microscopy Level 1 How the electron microscopy signal is generated from the sample True String BSE SE phase bright-field dark-field EM instrument Electron Microscopy Level 1 Make and model of the EM instrument used True String Protocol Link Electron Microscopy Level 1 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 Electron Microscopy Level 1 Name of software used to generate expression values. String True Pseudo Alignment Used is "Yes - Pseudo Alignment Used" String SizeX Electron Microscopy Level 1 Size of image: X dimension (in pixels). Integer >= 1 True String SizeY Electron Microscopy Level 1 Size of image: Y dimension (in pixels). Integer >= 1 True String SizeC Electron Microscopy Level 1 Number of channels. Integer >= 1 True String SizeZ Electron Microscopy Level 1 Size of image: Z dimension (in pixels). Integer >= 1 True String PhysicalSizeX Electron Microscopy Level 1 Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0. True String PhysicalSizeY Electron Microscopy Level 1 Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0. True String PhysicalSizeZ Electron Microscopy Level 1 Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0. True String EM dwell or exposure time Electron Microscopy Level 1 Duration in microseconds (µs) of electron beam data collection per pixel or frame False String EM voltage Electron Microscopy Level 1 Accelerating voltage in kiloelectronvolts (keV) False String EM beam current Electron Microscopy Level 1 Beam current in nanoamps (nA) False String EM spot size Electron Microscopy Level 1 Beam spot size in micrometers (µm) False String EM stage tilt Electron Microscopy Level 1 Physical stage tilt in degrees with respect to the electron beam False String EM signal processing Electron Microscopy Level 1 SNR improvement strategies used False String None line integration frame integration frame averaging EM contrast type Electron Microscopy Level 1,Electron Microscopy Level 2 Does the image use standard SEM contrast or TEM contrast False String SEM TEM Tile overlap X Electron Microscopy Level 1,Electron Microscopy Level 2 Percentage of image overlap to allow tile stitching in x direction True String Tile overlap Y Electron Microscopy Level 1,Electron Microscopy Level 2 Percentage of image overlap to allow tile stitching in x direction True String HTAN Parent Data File ID Electron Microscopy Level 2,Electron Microscopy Level 3,Electron Microscopy Level 4 HTAN Data File Identifier indicating the file(s) from which these files were derived True String Imaging Object Class Electron Microscopy Level 3 Defines the structure that the mask delineates True String nucleus cytoplasm plasma membrane whole cell spot Imaging Object Class Other Comment Electron Microscopy Level 4 Free text field (generally for QC comment) False Passed QC is "No - Channels QC" String PhysicalSizeXUnit Electron Microscopy Level 1 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 PhysicalSizeYUnit Electron Microscopy Level 1 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 PhysicalSizeZUnit Electron Microscopy Level 1 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 Imaging Object Class Other Electron Microscopy Level 3 Imaging Object Class Other False String Imaging Object Class Description Electron Microscopy Level 3 Free text description of object class [string] True Imaging Object Class is "Imaging Object Class Other" String