Specimen procedure types
Type-specific details of ex-vivo processing steps performed on a specimen set.
This family is still being refined and its fields may change between releases.
Table of contents
- Preparation: Initial handling of ex-vivo material, such as dissecting tissue for further processing.
Dissection - Sectioning: Cutting of tissue into sections or slices on a cryostat, vibratome, microtome or similar instrument.
Cryosectioning · Sectioning - Fixation and Preservation: Steps that fix, embed or cryopreserve specimens to preserve tissue for later processing.
Cryopreservation · Embedding · Fixation (immersion) - Clearing and Mounting: Rendering tissue transparent and mounting specimens for imaging.
Mounting · Tissue clearing - Labeling and Staining: Steps that label or stain molecular and structural targets in a specimen, including antigen retrieval, blocking, immunolabeling, in situ hybridization, dye loading, staining and washes.
Antigen retrieval · Blocking · Dye loading · Immunolabeling · In situ hybridization · Staining · Wash step - Tissue Processing: Chemical processing steps that prepare tissue for embedding, clearing or imaging, such as dehydration.
Dehydration - Generic: Specimen interventions that no specific specimen procedure type describes.
Generic intervention
Preparation
Initial handling of ex-vivo material, such as dissecting tissue for further processing.
Dissection
Separating tissue from the body or dividing it into regions of interest.
| Field | Description |
|---|---|
Instrument | Text. Dissection instrument used. |
Temperature | Quantity with unit. Temperature during dissection (e.g., 4 °C for ice-cold, 22 °C for room temperature). Units: °C, K. |
Duration | Quantity with unit. Time taken to complete the dissection. Units: s, min, h. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Processing medium | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Processing supply | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Other material | manual entry |
Stages: Dissection.
Sectioning
Cutting of tissue into sections or slices on a cryostat, vibratome, microtome or similar instrument.
Cryosectioning
Cutting frozen tissue on a cryostat. Use this rather than Sectioning whenever the tissue was frozen for cutting.
| Field | Description |
|---|---|
Section thickness | Quantity with unit. Nominal section thickness as set on the cryostat for this event; actual sections may deviate from the setting. Units: µm, mm, nm, m. |
Orientation | Text. Anatomical plane in which the tissue was cut; for an oblique cut, state the plane it deviates from and how. |
Number of sections | Integer. Total number of sections produced by this cutting event. Range: ≥ 0. |
Serial sectioning | Yes/no. Check if every cut section was retained (a complete collection), whether kept as one series or distributed across parallel series; leave unchecked if sections were discarded during collection. |
Section interval | Integer. Sampling interval of one collected series: each series contains every nth section (e.g., 6 means every 6th section). Enter 1 when a single complete series contains every section. Range: ≥ 1. |
Collection method | Choice. Technique by which the sections were collected off the knife: mounted directly onto slides, collected free-floating into wells or dishes, or transferred with a tape system. Choose Other for a technique not listed. Options: Direct mount, Free floating, Tape transfer, Other. |
Blade angle | Quantity with unit. Blade clearance angle set on the cutting instrument for this event. Units: °. |
Cutting speed | Quantity with unit. Blade advance speed set for this event. Units: µm/s, mm/s. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Embedding medium | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Cryoprotectant | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Processing supply | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Other material | manual entry |
Stages: Cryostat run, Collection, Storage.
Sectioning
Cutting tissue into sections at room or bath temperature, as with a vibratome. Thickness and orientation are required because nothing downstream can be interpreted without them.
| Field | Description |
|---|---|
Section thickness | Quantity with unit. Nominal section thickness as set on the cutting instrument for this event; actual sections may deviate from the setting. Units: µm, mm, nm, m. |
Orientation | Text. Anatomical plane in which the tissue was cut; for an oblique cut, state the plane it deviates from and how. |
Number of sections | Integer. Total number of sections produced by this event. Range: ≥ 0. |
Blade angle | Quantity with unit. Blade clearance angle set on the cutting instrument for this event. Units: °. |
Cutting speed | Quantity with unit. Blade advance speed set for this event. Units: µm/s, mm/s. |
Vibration amplitude | Quantity with unit. Lateral blade vibration amplitude set for this event; leave empty for instruments without a vibrating blade. Units: µm, mm, nm, m. |
Vibration frequency | Quantity with unit. Blade vibration frequency set for this event; leave empty for instruments without a vibrating blade. Units: Hz. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Embedding medium | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Processing supply | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Other material | manual entry |
Stages: Sectioning run, Collection, Storage.
Fixation and Preservation
Steps that fix, embed or cryopreserve specimens to preserve tissue for later processing.
Cryopreservation
Preparing and holding tissue frozen for later use.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Cryoprotectant | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Other material | manual entry |
Stages: Equilibration, Freezing.
Embedding
Setting tissue in a supporting medium such as paraffin, agarose, or OCT before cutting. The medium is recorded as a material.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Embedding medium | yes | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | |
| Processing reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Processing supply | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Other material | manual entry |
Stages: Infiltration, Embedding.
Fixation (immersion)
Preserving tissue by immersing it in fixative. Perfusion fixation through the circulation is a Procedure on the subject, not a Specimen procedure. Record the fixative itself as a material.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Fixative | yes | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | |
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Other material | manual entry |
Stages: Fixation, Wash.
Clearing and Mounting
Rendering tissue transparent and mounting specimens for imaging.
Mounting
Placing sections on slides under coverslips for imaging. The mounting medium is recorded as a material.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Mounting medium | stock: Histology reagent; catalog: Histology reagent; manual entry | ||
| Index-matching medium | stock: Histology reagent; catalog: Histology reagent; manual entry | ||
| Slide, coverslip, or mounting support | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Adhesive, cement, or sealant | stock: Adhesive or cement; catalog: Adhesive or cement; manual entry | ||
| Other material | manual entry |
Stages: Mounting, Curing.
Tissue clearing
Making tissue optically transparent for volumetric imaging. The clearing method is required, since duration and temperature are only interpretable against it.
| Field | Description |
|---|---|
Clearing method | Choice. Clearing method family used to render the tissue transparent. Solvent-based families (iDISCO+, 3DISCO, uDISCO, PEGASOS) shrink tissue and require solvent-tolerant optics and immersion media; hydrogel and aqueous families do not. Choose Other for a method family not listed. Options: CLARITY, PACT, SHIELD, CUBIC, ScaleS, iDISCO+, 3DISCO, uDISCO, PEGASOS, Other. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Clearing reagent | yes | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | |
| Permeabilization reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Index-matching medium | stock: Histology reagent; catalog: Histology reagent; manual entry | ||
| Other material | manual entry |
Stages: Permeabilization, Decolorization, Delipidation, Wash, Clearing, Index matching, Other.
Labeling and Staining
Steps that label or stain molecular and structural targets in a specimen, including antigen retrieval, blocking, immunolabeling, in situ hybridization, dye loading, staining and washes.
Antigen retrieval
Unmasking epitopes before immunolabeling, normally by heat or enzyme.
| Field | Description |
|---|---|
Retrieval method | Choice. Antigen retrieval strategy used. Options: Heat-induced (HIER), Enzymatic, Other. |
Temperature | Quantity with unit. Temperature during antigen retrieval. Units: °C, K, °F. |
Duration | Quantity with unit. Duration of the antigen retrieval step. Units: µs, ms, s, min, h. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Retrieval reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Retrieval, Wash.
Blocking
Blocking non-specific binding before labeling. Record the blocking solution as a material.
| Field | Description |
|---|---|
Blocking duration | Quantity with unit. Duration of the blocking step. Units: µs, ms, s, min, h. |
Temperature | Quantity with unit. Temperature during blocking. Units: °C, K, °F. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Blocking reagent | yes | stock: Histology reagent, Antibody or immunoreagent, Chemical reagent; catalog: Histology reagent, Antibody or immunoreagent, Chemical reagent; manual entry | |
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Blocking, Wash.
Dye loading
Loading a dye or indicator into tissue or cells. Record the dye as a material.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Stain or dye | yes | stock: Tracer or dye, Chemical reagent; catalog: Tracer or dye, Chemical reagent; manual entry | |
| Processing reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Loading, Washout.
Immunolabeling
Antibody-based labeling. Record the primary and secondary antibodies as materials, each with its dilution, and use stages for the incubation and wash sequence.
| Field | Description |
|---|---|
Labeling configuration | Choice. Physical configuration of the specimen during labeling: free-floating, slide-mounted, or whole-mount. Options: Free-floating, On slide, Whole-mount. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Blocking reagent | stock: Histology reagent, Antibody or immunoreagent, Chemical reagent; catalog: Histology reagent, Antibody or immunoreagent, Chemical reagent; manual entry | ||
| Permeabilization reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Primary immunolabeling reagent | yes | stock: Antibody or immunoreagent; catalog: Antibody or immunoreagent; manual entry | |
| Secondary immunolabeling reagent | stock: Antibody or immunoreagent; catalog: Antibody or immunoreagent; manual entry | ||
| Detection reagent | stock: Antibody or immunoreagent, Histology reagent; catalog: Antibody or immunoreagent, Histology reagent; manual entry | ||
| Stain or dye | stock: Tracer or dye, Chemical reagent; catalog: Tracer or dye, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Permeabilization, Blocking, Primary incubation, Wash, Secondary incubation, Detection, Counterstain.
In situ hybridization
Probe-based labeling of nucleic acid targets. Record the probes as materials and the hybridization and wash steps as stages.
| Field | Description |
|---|---|
Hybridization method | Choice. Hybridization chemistry used to detect the target transcripts. Options: RNAscope, HCR, Chromogenic ISH, FISH, Other. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Hybridization probe | yes | stock: Antibody or immunoreagent, Chemical reagent; catalog: Antibody or immunoreagent, Chemical reagent; manual entry | |
| Detection reagent | stock: Antibody or immunoreagent, Histology reagent; catalog: Antibody or immunoreagent, Histology reagent; manual entry | ||
| Blocking reagent | stock: Histology reagent, Antibody or immunoreagent, Chemical reagent; catalog: Histology reagent, Antibody or immunoreagent, Chemical reagent; manual entry | ||
| Stain or dye | stock: Tracer or dye, Chemical reagent; catalog: Tracer or dye, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Pretreatment, Prehybridization, Hybridization, Stringency wash, Amplification, Detection, Counterstain.
Staining
Applying a general stain, such as Nissl or a histochemical stain. It defines no fields of its own: record the stain in Material usage and the timing in stages.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Stain or dye | yes | stock: Tracer or dye, Chemical reagent; catalog: Tracer or dye, Chemical reagent; manual entry | |
| Processing reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Staining, Differentiation, Rinse, Bluing, Counterstain, Dehydration.
Wash step
A standalone wash. Record it separately only when the wash is worth its own entry; a wash inside a labeling run belongs in that run’s stages instead.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Wash solution | yes | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | |
| Other material | manual entry |
Stages: Wash.
Tissue Processing
Chemical processing steps that prepare tissue for embedding, clearing or imaging, such as dehydration.
Dehydration
Removing water through a graded solvent series, usually before embedding or clearing. The series itself is recorded as ordered stages with the solutions as materials.
This type has no type-specific fields. The record’s own fields and its material rows describe it.
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Dehydration reagent | yes | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | |
| Wash solution | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Processing reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Other material | manual entry |
Stages: Dehydration.
Generic
Specimen interventions that no specific specimen procedure type describes.
Generic intervention
Use this only when no specific type applies. The intervention method is required, and the description should say plainly what was done, because the type name tells another user nothing.
| Field | Description |
|---|---|
Intervention method | Text. What was done to the specimen, in the lab’s own words. |
Materials that can be recorded on this type:
| Material role | Required | Taken from | Complete when |
|---|---|---|---|
| Processing reagent | stock: Histology reagent, Chemical reagent; catalog: Histology reagent, Chemical reagent; manual entry | ||
| Active agent | stock: Pharmacological agent, Chemical reagent; catalog: Pharmacological agent, Chemical reagent; manual entry | ||
| Buffer | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Processing medium | stock: Physiological solution, Chemical reagent; catalog: Physiological solution, Chemical reagent; manual entry | ||
| Storage medium | stock: Physiological solution, Histology reagent; catalog: Physiological solution, Histology reagent; manual entry | ||
| Collection container | stock: Surgical disposable, Consumable device; catalog: Surgical disposable, Consumable device; manual entry | ||
| Processing supply | stock: Surgical disposable; catalog: Surgical disposable; manual entry | ||
| Other material | manual entry |
Stages: Processing.
API access
The same types are documented for API users, with property codes, versions and payload examples, on the SpecimenProcedure schemas API page.