HTAN Electron Microscopy

Electron microscopy data are divided into four primary levels:

Level	Definition	Example Data
1	Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage	tiff
2	Processed electron microscopy data as one OME-TIFF image per plane or montage	ome-tiff
3	Segmented electron microscopy data	am, tiff
4	Movies or other derived files from electron microscopy data	mp4, 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:

in a specific manifest; or
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.

Manifests
All Attributes

Manifest

▲

Description

▲

Electron Microscopy Level 1

Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage

Electron Microscopy Level 2

Processed electron microscopy data as one OME-TIFF image per plane or montage

Electron Microscopy Level 3

Segmented electron microscopy data as .am or .tiff formats

Electron Microscopy Level 4

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

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