SpecimenProcedure schemas

Type-specific details of ex-vivo processing steps performed on a specimen set.

This family is experimental: its schemas may change shape between releases without a version bump. Treat writes to these types as experimental.

How to use this family
Quick type map
Preparation
1. Dissection
Sectioning
1. Cryosectioning
2. Sectioning
Fixation and Preservation
Clearing and Mounting
1. Mounting
2. Tissue clearing
Labeling and Staining
Tissue Processing
1. Dehydration
Generic
1. Generic intervention

How to use this family

specimenprocedure: set type to a type code below and send its properties in details.
specimenproceduretemplate: set type to a type code below and send its properties in details.
Every version is published at https://www.brainstem.org/schemas/SpecimenProcedure/<Type>/<version>.json and never changes; https://www.brainstem.org/schemas/SpecimenProcedure/<Type>.json is the current version and https://www.brainstem.org/schemas/SpecimenProcedure/<Type>/ lists the versions. See Public schemas.
Quantities are objects {"value": <number>, "unit": "<code>"}. Property paths with [] are inside a repeatable list of rows. The server sets the schema version field itself.

Quick type map

Type code	Title	Group	Version	Required properties	Schema
`AntigenRetrieval`	Antigen retrieval	Labeling and Staining	1.0.1	none	1.0.1.json
`Blocking`	Blocking	Labeling and Staining	1.0.1	none	1.0.1.json
`Cryopreservation`	Cryopreservation	Fixation and Preservation	1.0.0	none	1.0.0.json
`Cryosectioning`	Cryosectioning	Sectioning	1.0.0	none	1.0.0.json
`Dehydration`	Dehydration	Tissue Processing	1.1.0	none	1.1.0.json
`Dissection`	Dissection	Preparation	1.0.1	none	1.0.1.json
`DyeLoading`	Dye loading	Labeling and Staining	1.0.0	none	1.0.0.json
`Embedding`	Embedding	Fixation and Preservation	1.0.0	none	1.0.0.json
`Fixation`	Fixation (immersion)	Fixation and Preservation	1.0.0	none	1.0.0.json
`GenericIntervention`	Generic intervention	Generic	1.0.0	none	1.0.0.json
`Immunolabeling`	Immunolabeling	Labeling and Staining	1.0.0	none	1.0.0.json
`InSituHybridization`	In situ hybridization	Labeling and Staining	1.0.0	none	1.0.0.json
`Mounting`	Mounting	Clearing and Mounting	1.0.0	none	1.0.0.json
`Sectioning`	Sectioning	Sectioning	1.0.0	none	1.0.0.json
`Staining`	Staining	Labeling and Staining	1.0.0	none	1.0.0.json
`TissueClearing`	Tissue clearing	Clearing and Mounting	1.0.0	none	1.0.0.json
`WashStep`	Wash step	Labeling and Staining	1.0.0	none	1.0.0.json

Preparation

Dissection

type code Dissection · version 1.0.1 · schema

Separating tissue from the body or dividing it into regions of interest.

Property	Title	Shape	Allowed values	Meaning
`instrument`	Instrument	text		Dissection instrument used.
`dissectionTemperature`	Temperature	quantity with unit	units `°C`, `K`; default `{"unit": "°C"}`	Temperature during dissection (e.g., 4 °C for ice-cold, 22 °C for room temperature).
`duration`	Duration	quantity with unit	units `s`, `min`, `h`; default `{"unit": "min"}`	Time taken to complete the dissection.

Illustrative payload:

{
    "instrument": "text",
    "dissectionTemperature": {
        "value": 1,
        "unit": "°C"
    }
}

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`Medium` (Processing medium)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Buffer` (Buffer)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)	`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`CollectionContainer` (Collection container)	`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`ProcessingSupply` (Processing supply)	`SurgicalDisposable`	`SurgicalDisposable`	yes
`Other` (Other material)			yes

Stages:

dissection_step (Dissection), no detail schema; repeatable

Sectioning

Cryosectioning

type code Cryosectioning · version 1.0.0 · schema

Cutting frozen tissue on a cryostat. Use this rather than Sectioning whenever the tissue was frozen for cutting.

Property	Title	Shape	Allowed values	Meaning
`thickness`	Section thickness	quantity with unit	units `µm`, `mm`, `nm`, `m`; default `{"unit": "µm"}`	Nominal section thickness as set on the cryostat for this event; actual sections may deviate from the setting.
`orientation`	Orientation	text		Anatomical plane in which the tissue was cut; for an oblique cut, state the plane it deviates from and how.
`nSections`	Number of sections	integer	≥ 0	Total number of sections produced by this cutting event.
`serialSectioning`	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.
`sectionInterval`	Section interval	integer	≥ 1	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.
`collectionMethod`	Collection method	choice	one of `direct_mount`, `free_floating`, `tape_transfer`, `other`	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.
`bladeAngle`	Blade angle	quantity with unit	units `°`; default `{"unit": "°"}`	Blade clearance angle set on the cutting instrument for this event.
`cuttingSpeed`	Cutting speed	quantity with unit	units `µm/s`, `mm/s`; default `{"unit": "mm/s"}`	Blade advance speed set for this event.

Illustrative payload:

{
    "thickness": {
        "value": 1,
        "unit": "µm"
    },
    "orientation": "text"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`EmbeddingMedium` (Embedding medium)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Cryoprotectant` (Cryoprotectant)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)	`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`CollectionContainer` (Collection container)	`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`ProcessingSupply` (Processing supply)	`SurgicalDisposable`	`SurgicalDisposable`	yes
`Other` (Other material)			yes

Stages:

cryostat_run (Cryostat run), no detail schema; repeatable
collection_step (Collection), no detail schema; repeatable
storage_step (Storage), no detail schema; repeatable

Sectioning

type code Sectioning · version 1.0.0 · schema

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.

Property	Title	Shape	Allowed values	Meaning
`thickness`	Section thickness	quantity with unit	units `µm`, `mm`, `nm`, `m`; default `{"unit": "µm"}`	Nominal section thickness as set on the cutting instrument for this event; actual sections may deviate from the setting.
`orientation`	Orientation	text		Anatomical plane in which the tissue was cut; for an oblique cut, state the plane it deviates from and how.
`nSections`	Number of sections	integer	≥ 0	Total number of sections produced by this event.
`bladeAngle`	Blade angle	quantity with unit	units `°`; default `{"unit": "°"}`	Blade clearance angle set on the cutting instrument for this event.
`cuttingSpeed`	Cutting speed	quantity with unit	units `µm/s`, `mm/s`; default `{"unit": "mm/s"}`	Blade advance speed set for this event.
`vibrationAmplitude`	Vibration amplitude	quantity with unit	units `µm`, `mm`, `nm`, `m`; default `{"unit": "mm"}`	Lateral blade vibration amplitude set for this event; leave empty for instruments without a vibrating blade.
`vibrationFrequency`	Vibration frequency	quantity with unit	units `Hz`; default `{"unit": "Hz"}`	Blade vibration frequency set for this event; leave empty for instruments without a vibrating blade.

Illustrative payload:

{
    "thickness": {
        "value": 1,
        "unit": "µm"
    },
    "orientation": "text"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`Buffer` (Buffer)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`EmbeddingMedium` (Embedding medium)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)	`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`CollectionContainer` (Collection container)	`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`ProcessingSupply` (Processing supply)	`SurgicalDisposable`	`SurgicalDisposable`	yes
`Other` (Other material)			yes

Stages:

sectioning_run (Sectioning run), no detail schema; repeatable
collection_step (Collection), no detail schema; repeatable
storage_step (Storage), no detail schema; repeatable

Fixation and Preservation

Cryopreservation

type code Cryopreservation · version 1.0.0 · schema

Preparing and holding tissue frozen for later use.

This type has no type-specific properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Fields hidden by the web form for this type (leave empty): target_regions, target_regions_atlas.

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`Cryoprotectant` (Cryoprotectant)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)	`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`CollectionContainer` (Collection container)	`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`Other` (Other material)			yes

Stages:

equilibration_step (Equilibration), no detail schema; repeatable
freezing_step (Freezing), no detail schema; repeatable

Embedding

type code Embedding · version 1.0.0 · schema

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 properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`EmbeddingMedium` (Embedding medium)	yes	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`ProcessingReagent` (Processing reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`CollectionContainer` (Collection container)		`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`ProcessingSupply` (Processing supply)		`SurgicalDisposable`	`SurgicalDisposable`	yes
`Other` (Other material)				yes

Stages:

infiltration_step (Infiltration), no detail schema; repeatable
embedding_step (Embedding), no detail schema; repeatable

Fixation (immersion)

type code Fixation · version 1.0.0 · schema

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 properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`Fixative` (Fixative)	yes	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)		`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`Other` (Other material)				yes

Stages:

fixation_step (Fixation), no detail schema; repeatable
wash_step (Wash), no detail schema; repeatable

Clearing and Mounting

Mounting

type code Mounting · version 1.0.0 · schema

Placing sections on slides under coverslips for imaging. The mounting medium is recorded as a material.

This type has no type-specific properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`MountingMedium` (Mounting medium)	`HistologyReagent`	`HistologyReagent`	yes
`IndexMatchingMedium` (Index-matching medium)	`HistologyReagent`	`HistologyReagent`	yes
`MountingComponent` (Slide, coverslip, or mounting support)	`SurgicalDisposable`	`SurgicalDisposable`	yes
`AdhesiveSealant` (Adhesive, cement, or sealant)	`AdhesiveCement`	`AdhesiveCement`	yes
`Other` (Other material)			yes

Stages:

mounting_step (Mounting), no detail schema; repeatable
curing_step (Curing), no detail schema; repeatable

Tissue clearing

type code TissueClearing · version 1.0.0 · schema

Making tissue optically transparent for volumetric imaging. The clearing method is required, since duration and temperature are only interpretable against it.

Property	Title	Shape	Required	Allowed values	Meaning
`method`	Clearing method	choice		one of `clarity`, `pact`, `shield`, `cubic`, `scales`, `idisco`, `3disco`, `udisco`, `pegasos`, `other`	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.

Illustrative payload:

{
    "method": "clarity"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`ClearingReagent` (Clearing reagent)	yes	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`PermeabilizationReagent` (Permeabilization reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`IndexMatchingMedium` (Index-matching medium)		`HistologyReagent`	`HistologyReagent`	yes
`Other` (Other material)				yes

Stages:

permeabilization (Permeabilization), no detail schema; repeatable
decolorization (Decolorization), no detail schema; repeatable
delipidation (Delipidation), no detail schema; repeatable
wash (Wash), no detail schema; repeatable
clearing (Clearing), no detail schema; repeatable
index_matching (Index matching), no detail schema; repeatable
other (Other), no detail schema; repeatable

Labeling and Staining

Antigen retrieval

type code AntigenRetrieval · version 1.0.1 · schema

Unmasking epitopes before immunolabeling, normally by heat or enzyme.

Property	Title	Shape	Allowed values	Meaning
`method`	Retrieval method	choice	one of `heat_induced_hier`, `enzymatic`, `other`	Antigen retrieval strategy used.
`temperature`	Temperature	quantity with unit	units `°C`, `K`, `°F`; default `{"unit": "°C"}`	Temperature during antigen retrieval.
`duration`	Duration	quantity with unit	units `µs`, `ms`, `s`, `min`, `h`; default `{"unit": "min"}`	Duration of the antigen retrieval step.

Illustrative payload:

{
    "method": "heat_induced_hier",
    "temperature": {
        "value": 1,
        "unit": "°C"
    }
}

Fields hidden by the web form for this type (leave empty): target_regions, target_regions_atlas.

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`RetrievalReagent` (Retrieval reagent)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)			yes

Stages:

retrieval_step (Retrieval), no detail schema; repeatable
wash_step (Wash), no detail schema; repeatable

Blocking

type code Blocking · version 1.0.1 · schema

Blocking non-specific binding before labeling. Record the blocking solution as a material.

Property	Title	Shape	Required	Allowed values	Meaning
`duration`	Blocking duration	quantity with unit		units `µs`, `ms`, `s`, `min`, `h`; default `{"unit": "h"}`	Duration of the blocking step.
`temperature`	Temperature	quantity with unit		units `°C`, `K`, `°F`; default `{"unit": "°C"}`	Temperature during blocking.

Illustrative payload:

{
    "duration": {
        "value": 1,
        "unit": "h"
    },
    "temperature": {
        "value": 1,
        "unit": "°C"
    }
}

Fields hidden by the web form for this type (leave empty): target_regions, target_regions_atlas.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`BlockingReagent` (Blocking reagent)	yes	`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

blocking_step (Blocking), no detail schema; repeatable
wash_step (Wash), no detail schema; repeatable

Dye loading

type code DyeLoading · version 1.0.0 · schema

Loading a dye or indicator into tissue or cells. Record the dye as a material.

This type has no type-specific properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`StainDye` (Stain or dye)	yes	`TracerDye`, `ChemicalReagent`	`TracerDye`, `ChemicalReagent`	yes
`ProcessingReagent` (Processing reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

loading_step (Loading), no detail schema; repeatable
washout_step (Washout), no detail schema; repeatable

Immunolabeling

type code Immunolabeling · version 1.0.0 · schema

Antibody-based labeling. Record the primary and secondary antibodies as materials, each with its dilution, and use stages for the incubation and wash sequence.

Property	Title	Shape	Required	Allowed values	Meaning
`labelingConfiguration`	Labeling configuration	choice		one of `free_floating`, `on_slide`, `whole_mount`	Physical configuration of the specimen during labeling: free-floating, slide-mounted, or whole-mount.

Illustrative payload:

{
    "labelingConfiguration": "free_floating"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`BlockingReagent` (Blocking reagent)		`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	yes
`PermeabilizationReagent` (Permeabilization reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`PrimaryLabel` (Primary immunolabeling reagent)	yes	`ImmunoReagent`	`ImmunoReagent`	yes
`SecondaryLabel` (Secondary immunolabeling reagent)		`ImmunoReagent`	`ImmunoReagent`	yes
`DetectionReagent` (Detection reagent)		`ImmunoReagent`, `HistologyReagent`	`ImmunoReagent`, `HistologyReagent`	yes
`StainDye` (Stain or dye)		`TracerDye`, `ChemicalReagent`	`TracerDye`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

permeabilization_step (Permeabilization), no detail schema; repeatable
blocking_step (Blocking), no detail schema; repeatable
primary_incubation (Primary incubation), no detail schema; repeatable
wash_step (Wash), no detail schema; repeatable
secondary_incubation (Secondary incubation), no detail schema; repeatable
detection_step (Detection), no detail schema; repeatable
counterstain_step (Counterstain), no detail schema; repeatable

In situ hybridization

type code InSituHybridization · version 1.0.0 · schema

Probe-based labeling of nucleic acid targets. Record the probes as materials and the hybridization and wash steps as stages.

Property	Title	Shape	Required	Allowed values	Meaning
`method`	Hybridization method	choice		one of `rnascope`, `hcr`, `chromogenic_ish`, `fish`, `other`	Hybridization chemistry used to detect the target transcripts.

Illustrative payload:

{
    "method": "rnascope"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`HybridizationProbe` (Hybridization probe)	yes	`ImmunoReagent`, `ChemicalReagent`	`ImmunoReagent`, `ChemicalReagent`	yes
`DetectionReagent` (Detection reagent)		`ImmunoReagent`, `HistologyReagent`	`ImmunoReagent`, `HistologyReagent`	yes
`BlockingReagent` (Blocking reagent)		`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	`HistologyReagent`, `ImmunoReagent`, `ChemicalReagent`	yes
`StainDye` (Stain or dye)		`TracerDye`, `ChemicalReagent`	`TracerDye`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

pretreatment_step (Pretreatment), no detail schema; repeatable
prehybridization_step (Prehybridization), no detail schema; repeatable
hybridization_step (Hybridization), no detail schema; repeatable
stringency_wash (Stringency wash), no detail schema; repeatable
amplification_step (Amplification), no detail schema; repeatable
detection_step (Detection), no detail schema; repeatable
counterstain_step (Counterstain), no detail schema; repeatable

Staining

type code Staining · version 1.0.0 · schema

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 properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`StainDye` (Stain or dye)	yes	`TracerDye`, `ChemicalReagent`	`TracerDye`, `ChemicalReagent`	yes
`ProcessingReagent` (Processing reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Buffer` (Buffer)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

staining_step (Staining), no detail schema; repeatable
differentiation_step (Differentiation), no detail schema; repeatable
rinse_step (Rinse), no detail schema; repeatable
bluing_step (Bluing), no detail schema; repeatable
counterstain_step (Counterstain), no detail schema; repeatable
dehydration_step (Dehydration), no detail schema; repeatable

Wash step

type code WashStep · version 1.0.0 · schema

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 properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Fields hidden by the web form for this type (leave empty): target_regions, target_regions_atlas.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	Max	From stock types	From catalog types	Manual	Complete when
`WashSolution` (Wash solution)	yes		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Other` (Other material)					yes

Stages:

wash_step (Wash), no detail schema; repeatable

Tissue Processing

Dehydration

type code Dehydration · version 1.1.0 · schema

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 properties: send an empty object. Everything meaningful is recorded on the record itself or on its material usage rows.

Fields hidden by the web form for this type (leave empty): target_regions, target_regions_atlas.

Materials (material usage rows) allowed on this type:

Role (`type`)	Required	From stock types	From catalog types	Manual
`DehydrationReagent` (Dehydration reagent)	yes	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`WashSolution` (Wash solution)		`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`ProcessingReagent` (Processing reagent)		`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`Other` (Other material)				yes

Stages:

dehydration_step (Dehydration), no detail schema; repeatable

Generic

Generic intervention

type code GenericIntervention · version 1.0.0 · schema

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.

Property	Title	Shape	Required	Allowed values	Meaning
`interventionMethod`	Intervention method	text			What was done to the specimen, in the lab’s own words.

Illustrative payload:

{
    "interventionMethod": "text"
}

Materials (material usage rows) allowed on this type:

Role (`type`)	From stock types	From catalog types	Manual
`ProcessingReagent` (Processing reagent)	`HistologyReagent`, `ChemicalReagent`	`HistologyReagent`, `ChemicalReagent`	yes
`ActiveAgent` (Active agent)	`PharmacologicalAgent`, `ChemicalReagent`	`PharmacologicalAgent`, `ChemicalReagent`	yes
`Buffer` (Buffer)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`Medium` (Processing medium)	`PhysiologicalSolution`, `ChemicalReagent`	`PhysiologicalSolution`, `ChemicalReagent`	yes
`StorageMedium` (Storage medium)	`PhysiologicalSolution`, `HistologyReagent`	`PhysiologicalSolution`, `HistologyReagent`	yes
`CollectionContainer` (Collection container)	`SurgicalDisposable`, `ConsumableDevice`	`SurgicalDisposable`, `ConsumableDevice`	yes
`ProcessingSupply` (Processing supply)	`SurgicalDisposable`	`SurgicalDisposable`	yes
`Other` (Other material)			yes

Stages:

processing_step (Processing), no detail schema; repeatable

SpecimenProcedure schemas

Table of contents

How to use this family

Quick type map

Preparation

Dissection

Sectioning

Cryosectioning

Sectioning

Fixation and Preservation

Cryopreservation

Embedding

Fixation (immersion)

Clearing and Mounting

Mounting

Tissue clearing

Labeling and Staining

Antigen retrieval

Blocking

Dye loading

Immunolabeling

In situ hybridization

Staining

Wash step

Tissue Processing

Dehydration

Generic

Generic intervention