Annotation Classes

Annotation Classes#

This document provides an overview of the annotation classes used in our dataset. Each zarr crop contains multiple scales for different organelles, if annotated. Additionally, there is a special multiscale named all that aggregates all annotated classes.

Classes are categorized as either atomic classes or group classes:

  • Atomic Classes represent individual organelle components.

  • Group Classes are sets of atomic classes grouped under a common category.

Group classes reference their constituent atomic classes through the group_id.

Table of Contents#

  • Multiscale Structure

  • Class Categories - Atomic Classes - Group Classes

  • Detailed Class Descriptions

  • Aliases

  • Examples

Multiscale Structure#

In each zarr crop, annotations are organized into multiple scales: - Organelle-specific scales: Each annotated organelle has its own scale. - All-inclusive scale: The all scale includes annotations for all classes.

This hierarchical structure facilitates efficient data navigation and retrieval based on specific or broad annotation needs.

Class Categories#

Atomic Classes represent the fundamental components of cellular structures. Each atomic class is defined with a unique identifier and descriptive properties. Group Classes define broader categories by combining multiple atomic classes into a set. They are useful for high-level analysis and visualization.

Challenge vs. CellMap Class Usage#

The table below lists all annotation classes recognized by the CellMap Project Team.

Classes highlighted in green or blue are included in the current segmentation challenge: - Green denotes classes that are integrated in the instance evaluations - Blue denotes classes that are integrated in the semantic evaluations

Other classes are part of the broader CellMap ontology and may appear in future challenges or datasets.

Detailed Class Descriptions#

Below is a comprehensive list of atomic and group classes, along with an indication of whether they are used in the current challenge.

Aliases#

Some classes may have aliases for compatibility or alternative naming conventions. These are listed in the Alias column of the table above.

Examples#

  • Nucleus (nuc): Comprised of multiple components including the nuclear envelope membrane (ne_mem), nuclear pores (np_out, np_in), heterochromatin (hchrom), euchromatin (echrom), nucleoplasm (nucpl), and nucleolus (nucleo).

  • Mitochondria (mito): Includes the mitochondrial membrane (mito_mem), mitochondrial lumen (mito_lum), and mitochondrial ribosome (mito_ribo).

  • Endoplasmic Reticulum (er): A collective class that encompasses various ER components such as the ER membrane (er_mem), ER lumen (er_lum), and ER exit site (eres_mem, eres_lum).

For detailed information on each class and their relationships, refer to the table above.

Contents