CryoET Data Portal Ontology (CDPO)

The CryoET Data Portal Ontology (CDPO) describes non-biological and non-relevant components observed in cryo-electron tomography (cryo-ET) data, including sample support materials, contamination, artifacts, and fiducial markers.

Property

Value

Prefix

CDPO

License

MIT

Upper Ontology

BFO 2.0

Source

github.com/uermel/cdpo

Terms

Sample Support Components

ID

Name

Definition

CDPO:0000002

sample support component

Any component of the specimen support used in electron microscopy sample preparation.

CDPO:0000003

sample support material

Any component of the specimen support.

CDPO:0000004

electron microscopy grid

Any part of the metal sample support grid of an electron microscopy specimen.

CDPO:0000005

support film

Any part of the thin support applied to an electron microscopy grid.

CDPO:0000006

carbon support film

Any part of the thin support (amorphous carbon, graphene or graphene oxide) applied to an electron microscopy grid.

CDPO:0000007

holey carbon film

Any part of a holey carbon support material on an electron microscopy grid.

CDPO:0000008

lacey carbon film

Any part of a lacey carbon support material on an electron microscopy grid.

CDPO:0000009

gold support film

Any part of the thin support (gold) applied to an electron microscopy grid.

CDPO:0000010

holey gold film

Any part of a holey gold support material on an electron microscopy grid.

CDPO:0000011

support film fragment

Any detached part of the sample support film.

Contamination types

ID

Name

Definition

CDPO:0000013

contamination

Unwanted material deposited on or near the specimen that is not part of the biological sample.

CDPO:0000014

ice particle contamination

Crystalline or amorphous ice particles deposited on the specimen from atmospheric moisture.

CDPO:0000015

sputter particle contamination

Metal or other particles deposited from sputtering during FIB milling or coating processes.

CDPO:0000016

leopard skin contamination

A pattern of contamination or damage characterized by irregular spots on the specimen surface, typically from beam damage or devitrification.

Sample Artifact Regions

ID

Name

Definition

CDPO:0000017

sample artifact region

Any unintended alteration or feature in the specimen caused by sample preparation or imaging.

CDPO:0000018

non-vitreous region

An area of the specimen where the ice has crystallized rather than remaining in a vitrified (amorphous) state.

CDPO:0000019

dose-damaged region

An area of the specimen that has been altered due to excessive electron dose exposure.

CDPO:0000021

curtaining artifact region

Vertical striping pattern in FIB-milled lamellae caused by differential milling rates.

CDPO:0000022

sample tear

Physical discontinuity in the specimen caused by mechanical stress during handling or imaging.

Fiducial Markers

ID

Name

Definition

CDPO:0000023

fiducial marker

A reference marker used for alignment during tomographic reconstruction.

CDPO:0000024

gold fiducial nanoparticle

Gold nanoparticles added to the specimen surface to serve as alignment markers for tomographic reconstruction.

CDPO:0000025

gold CLEM label

Gold particles used as correlative light and electron microscopy markers to identify specific locations.

Tomographic Image Artifacts

ID

Name

Definition

CDPO:0000026

tomographic image artifact

A feature in a tomographic image that arises from data acquisition or processing rather than the specimen itself.

CDPO:0000027

tomographic reconstruction artifact

A feature in the reconstructed tomogram that arises from the reconstruction process rather than the specimen.

CDPO:0000028

unreconstructed region

An area of the tomogram that could not be properly reconstructed, typically due to missing wedge effects.

CDPO:0000029

streak artifact

Linear artifacts radiating from high-contrast features, caused by limited tilt range or alignment errors.

CDPO:0000030

sample charging artifact

Image distortion caused by electrostatic charge accumulation on the specimen.

CDPO:0000031

laser phase plate off-plane artifact

Image artifact resulting from misalignment of the laser phase plate out of the focal plane.

CDPO:0000032

laser phase plate off-node artifact

Image artifact resulting from the laser phase plate being positioned away from the optimal node position.

Other

ID

Name

Definition

CDPO:0000001

sample

The material of interest being studied, typically biological in nature, that is contained within and imaged as part of the specimen.

CDPO:0000012

vacuum region

The empty space surrounding the specimen in the tomogram, representing areas with no material.

CDPO:0000020

protein aggregate

Aggregated or denatured protein material that is not representative of native biological structures.

CDPO:0000033

tomogram edge

The boundary of the reconstructed tomogram volume.