Specimen model

Table of contents

1. Introduction
2. Fields
3. Types of specimens
4. Permissions
5. API access

Introduction

A specimen is one individually trackable item inside a specimen set: a single slice, section, well, culture item, organoid or tissue piece. Specimens give you per-item granularity when you need it. A set that does not need per-item tracking simply records an item count and creates no specimens.

A specimen is not the batch (that is the specimen set), not a live animal (that is the subject), and not a processing event. The processing history that drives a specimen’s state is recorded as specimen procedures on the set, which can target the whole set or specific specimens. Specimen logs, experimental interfaces and material usages can also target specific specimens of a set.

This model with its direct connections only: drag to pan, Ctrl + scroll to zoom, click a model to select it, use the chevron to see its fields.

Fields

Field	Description
Specimen set	The specimen set this item belongs to (required).
Local identifier	Stable identifier of the specimen within its set (required; string; maximum length: 100 characters; must be unique within the specimen set). Example: “S01”, “A3” (a well), “slice_04”
Type	Kind of item (required; default: Other). Selected from predefined types. See options below.
Status	Current availability of the item (required; default: Available). Choices: Planned, Available, In use, Reserved, Consumed, Discarded, Lost. Same vocabulary as the specimen set.
Quality	Quality assessment of the item. Choices: Excellent, Good, Fair, Poor, Not assessed.
Laterality	Which side of the brain or body the item comes from. Choices: Left, Right, Bilateral, Not applicable.
Order	Ordering of the item within the set (number; default 0). Example: the position of a section in the series.
Source specimen	The specimen this item was derived from, if applicable. Lineage must stay acyclic.
Preparation conditions	The set’s starting conditions plus the conditions added by specimen procedures on the whole set or on this item (read-only; recomputed automatically). Choices: Fixed, Cryoprotected / frozen, Embedded, Cleared, Stained / labelled, Mounted; none means fresh / unprocessed.
Storage location	Current physical storage location, container or slot (string; maximum length: 100 characters). Example: “Slide box 7, slot 12”
Storage conditions	Current storage conditions, such as temperature and medium (string; maximum length: 100 characters).
Termination date and time	When the item was consumed, discarded, lost or otherwise terminated.
Notes	Free-text notes about the item.
Type specific fields	Fields that depend on the selected type, such as the thickness or position of a slice or section. See the Specimen types schema.

Types of specimens

These are the available type options. See the schema for field details: Specimen types.

Slice: One slice of a slice series, typically a thick acute or organotypic slice.

Section: One thin histological section of a section series.

Well: One well of a well plate.

Culture item: One item of a culture, such as a dish or an insert.

Organoid: One organoid of an organoid batch.

Tissue piece: One piece of tissue, such as a dissected block.

Other: An item that does not fit the types above.

Permissions

Specimens inherit permissions through their specimen set, and so from the projects of that set.

Visit the permissions page to learn more.

API access

The API allows for programmable access to specimens. Learn more about the specimens’ fields and data structure on the Specimen API page.