Neuroglancer models

These are the Neuroglancer models that represent a mapping from the actual database tables to python classes, or ORM. (ORM: object relational mapping)

class neuroglancer.models.AlignmentScore(*args, **kwargs)

A model that holds the alignment score data.

Parameters: id (Auto) – ID

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.AnnotationAbstract(*args, **kwargs)

Abstract model for the 3 new annotation data models

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id

class neuroglancer.models.AnnotationArchive(active, created, id, animal, neuroglancer_model, brain_region, annotator, annotation_type, updated)

Parameters

active (Boolean) – DB column = active
created (DateTime) – DB column = created
id (BigAuto) – id
animal_id (ForeignKey) – DB column = FK_prep_id
neuroglancer_model_id (ForeignKey) – DB column = FK_state_id
brain_region_id (ForeignKey) – DB column = FK_structure_id
annotator_id (ForeignKey) – DB column = FK_annotator_id
annotation_type (Enum) – annotation type
updated (DateTime) – updated

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.AnnotationPointArchive(*args, **kwargs)

This class is for an archive of annotation points

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id
polygon_index (Char length=40) – polygon index
point_order (Integer) – point order
source (Char length=255) – source
cell_type_id (ForeignKey) – DB column = FK_cell_type_id
archive_id (ForeignKey) – DB column = FK_archive_set_id

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.AnnotationSession(*args, **kwargs)

This model describes a user session in Neuroglancer.

Parameters

active (Boolean) – DB column = active
created (DateTime) – DB column = created
id (BigAuto) – id
animal_id (ForeignKey) – DB column = FK_prep_id
neuroglancer_model_id (ForeignKey) – DB column = FK_state_id
brain_region_id (ForeignKey) – DB column = FK_structure_id
annotator_id (ForeignKey) – DB column = FK_annotator_id
annotation_type (Enum) – annotation type
updated (DateTime) – updated

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.AnnotationStatus(id)

Parameters: id (Auto) – ID

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.ArchiveSet(*args, **kwargs)

This class model is for set of archives. It gets used by the AnnotationPointArchive.

Parameters

active (Boolean) – DB column = active
created (DateTime) – DB column = created
id (BigAuto) – id
annotation_session_id (ForeignKey) – DB column = FK_session_id

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.AtlasToBeth(*args, **kwargs)

A model that holds the alignment score data. This is another version of the alignment score and needs to be renamed.

Parameters: id (Auto) – ID

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.BrainRegion(*args, **kwargs)

This class model is for the brain regions or structures in the brain.

Parameters

active (Boolean) – DB column = active
created (DateTime) – DB column = created
id (BigAuto) – id
abbreviation (Char length=200) – abbreviation
description (Text length=2001) – description
color (PositiveInteger) – color
hexadecimal (Char length=7) – hexadecimal

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.BrainShape(*args, **kwargs)

This class will hold the numpy data for a brain region.

Parameters

active (Boolean) – DB column = active
created (DateTime) – DB column = created
id (BigAuto) – id
animal_id (ForeignKey) – DB column = prep_id
brain_region_id (ForeignKey) – DB column = FK_structure_id
dimensions (Char length=50) – dimensions
xoffset (Float) – xoffset
yoffset (Float) – yoffset
zoffset (Float) – zoffset
numpy_data (Text) – Array (pickle)

exception DoesNotExist

exception MultipleObjectsReturned

midsection()

This is a helper method to show what the mid part of a brain region will look like.

Returns: the HTML pointing to the thumbnail of the mid part of the brain region.

class neuroglancer.models.CellType(*args, **kwargs)

Model corresponding to the cell type table in the database

Parameters

id (BigAuto) – id
cell_type (Char length=200) – cell type
description (Text length=2001) – description
active (Integer) – active
created (DateTime) – created

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.MarkedCell(*args, **kwargs)

This model is for the marked cell points entered in Neuroglancer.

Inheritance

AnnotationAbstract

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id
source (Char length=25) – source
cell_type_id (ForeignKey) – DB column = FK_cell_type_id

exception DoesNotExist

exception MultipleObjectsReturned

class SourceChoices(value): An enumeration.

class neuroglancer.models.MarkedCellWorkflow(*args, **kwargs)

This model is for the marked cell points workflow entered in Neuroglancer.

Inheritance

MarkedCells

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id
source (Char length=25) – source
cell_type_id (ForeignKey) – DB column = FK_cell_type_id

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.Points(*args, **kwargs)

Model corresponding to the annotation points table in the database

Parameters

id (BigAuto) – id
url (JSON) – Neuroglancer State
owner_id (ForeignKey) – DB column = person_id
public (Boolean) – DB column = active
readonly (Boolean) – Read only
created (DateTime) – created
updated (DateTime) – updated
user_date (Char length=25) – user date
comments (Char length=255) – comments

exception DoesNotExist

exception MultipleObjectsReturned

class neuroglancer.models.PolygonSequence(*args, **kwargs)

This model is for the polygons drawn by an anatomist in Neuroglancer.

Inheritance

AnnotationAbstract

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id
polygon_index (Char length=40) – polygon index
point_order (Integer) – point order
source (Char length=25) – source

exception DoesNotExist

exception MultipleObjectsReturned

class SourceChoices(value): An enumeration.

class neuroglancer.models.StructureCom(*args, **kwargs)

This model is for the COMs for a structure (brain region). They are usually entered by an anatomist in Neuroglancer.

Inheritance

AnnotationAbstract

Parameters

id (BigAuto) – id
x (Decimal) – X (um)
y (Decimal) – Y (um)
z (Decimal) – Z (um)
annotation_session_id (ForeignKey) – DB column = FK_session_id
source (Char length=25) – source

exception DoesNotExist

exception MultipleObjectsReturned

class SourceChoices(value): An enumeration.

class neuroglancer.models.UrlModel(*args, **kwargs)

Model corresponding to the neuroglancer json states stored in the neuroglancer_url table. This name was used as the original verion of Neuroglancer stored all the data in the URL.

Parameters

id (BigAuto) – id
url (JSON) – Neuroglancer State
owner_id (ForeignKey) – DB column = person_id
public (Boolean) – DB column = active
readonly (Boolean) – Read only
created (DateTime) – created
updated (DateTime) – updated
user_date (Char length=25) – user date
comments (Char length=255) – comments

exception DoesNotExist

exception MultipleObjectsReturned

property animal

Find the animal within the url between data/ and /neuroglancer_data: data/MD589/neuroglancer_data/C1

Returns: the first match if found, otherwise NA