HTAN Electron Microscopy

Electron microscopy data are divided into four primary levels:

LevelDefinitionExample Data
1Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montagetiff
2Processed electron microscopy data as one OME-TIFF image per plane or montageome-tiff
3Segmented electron microscopy dataam, tiff
4Movies or other derived files from electron microscopy datamp4, csv

Attributes

WARNING: Manifests provided on this page are for reference only. DO NOT USE THESE MANIFESTS FOR DATA SUBMISSION.

Directions

The interactive tables below are provided to help users understand the HTAN Data Model. The tables allow a user to view, search or download attributes either:

  1. in a specific manifest; or
  2. in all manifests represented on this page.

To view a specific manifest, click on the link in the Manifests tab. The manifest will appear in a new tab on the page. Navigate to the new tab to search for attributes or download the manifest.
To search for attributes among all manifests, navigate to the All Attributes tab and use the search box provided at the top of the tab. All attributes can also be downloaded as a csv file.

Manifest
Description
Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage
Processed electron microscopy data as one OME-TIFF image per plane or montage
Segmented electron microscopy data as .am or .tiff formats
Movies or other derived files from electron microscopy data
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
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