Index

A

actions (neuroglancer.admin.ArchiveSetAdmin attribute) add_com() (neuroglancer.annotation_manager.AnnotationManager method) add_polygons() (neuroglancer.annotation_manager.AnnotationManager method) add_volumes() (neuroglancer.annotation_manager.AnnotationManager method) align_atlas() (in module neuroglancer.atlas) AlignmentScore (class in neuroglancer.models) AlignmentScore.DoesNotExist AlignmentScore.MultipleObjectsReturned Animal (class in brain.models) animal (neuroglancer.models.UrlModel property) Animal.DoesNotExist Animal.MultipleObjectsReturned AnimalAdmin (class in brain.admin) AnimalChoiceField (class in brain.forms) AnimalDetail (class in brain.views) AnimalForm (class in brain.forms) AnimalForm.Meta (class in brain.forms) AnimalList (class in brain.views) AnimalSerializer (class in brain.serializers) AnnotationAbstract (class in neuroglancer.models) AnnotationArchive (class in neuroglancer.models) AnnotationArchive.DoesNotExist AnnotationArchive.MultipleObjectsReturned AnnotationManager (class in neuroglancer.annotation_manager)

AnnotationPointArchive (class in neuroglancer.models) AnnotationPointArchive.DoesNotExist AnnotationPointArchive.MultipleObjectsReturned AnnotationSerializer (class in neuroglancer.serializers) AnnotationSession (class in neuroglancer.models) AnnotationSession.DoesNotExist AnnotationSession.MultipleObjectsReturned AnnotationSessionAdmin (class in neuroglancer.admin) AnnotationStatus (class in neuroglancer.models) AnnotationStatus.DoesNotExist AnnotationStatus.MultipleObjectsReturned apply_scales_to_annotation_rows() (in module neuroglancer.views) archive_and_insert_annotations() (neuroglancer.annotation_manager.AnnotationManager method) archive_annotations() (neuroglancer.annotation_manager.AnnotationManager method) ArchiveSet (class in neuroglancer.models) ArchiveSet.DoesNotExist ArchiveSet.MultipleObjectsReturned ArchiveSetAdmin (class in neuroglancer.admin) AtlasAdminModel (class in brain.admin) AtlasAdminModel.Media (class in brain.admin) AtlasModel (class in brain.models) AtlasToBeth (class in neuroglancer.models) AtlasToBeth.DoesNotExist AtlasToBeth.MultipleObjectsReturned

B

base_fields (brain.forms.AnimalForm attribute) brain.admin module brain.forms module brain.models module brain.serializers module brain.views module

brain_to_atlas_transform() (in module neuroglancer.atlas) BrainRegion (class in neuroglancer.models) BrainRegion.DoesNotExist BrainRegion.MultipleObjectsReturned BrainRegionAdmin (class in neuroglancer.admin) BrainRegionSerializer (class in neuroglancer.serializers) BrainRegionSerializer.Meta (class in neuroglancer.serializers) BrainShape (class in neuroglancer.models) BrainShape.DoesNotExist BrainShape.MultipleObjectsReturned

C

CellType (class in neuroglancer.models) CellType.DoesNotExist CellType.MultipleObjectsReturned CellTypeAdmin (class in neuroglancer.admin) change_list_template (neuroglancer.admin.MarkedCellWorkflowAdmin attribute) changelist_view() (brain.admin.SectionAdmin method) (neuroglancer.admin.MarkedCellWorkflowAdmin method) ComListSerializer (class in neuroglancer.serializers) CompletedTaskAdmin (class in neuroglancer.admin)

ContoursToVolume (class in neuroglancer.views) create() (neuroglancer.serializers.UrlSerializer method) create_marked_cell() (neuroglancer.annotation_manager.AnnotationManager method) create_new_archive() (neuroglancer.annotation_manager.AnnotationManager method) create_new_session() (neuroglancer.annotation_manager.AnnotationManager method) create_polygon_and_volume_uuids() (neuroglancer.views.GetVolume method) create_scene() (in module brain.forms) created_display() (neuroglancer.admin.BrainRegionAdmin method) (neuroglancer.admin.CellTypeAdmin method) (neuroglancer.admin.PointsAdmin method)

D

datetime_format() (in module neuroglancer.admin) declared_fields (brain.forms.AnimalForm attribute) delete_session() (in module neuroglancer.admin)

display_filter (neuroglancer.admin.CompletedTaskAdmin attribute) (neuroglancer.admin.TaskAdmin attribute) drilldown_link() (neuroglancer.admin.MarkedCellWorkflowAdmin method)

E

exclude (neuroglancer.admin.UrlModelAdmin attribute)

export_as_csv() (brain.admin.ExportCsvMixin method) ExportCsvMixin (class in brain.admin)

F

fields (brain.forms.AnimalForm.Meta attribute) (neuroglancer.admin.ArchiveSetAdmin attribute) (neuroglancer.serializers.BrainRegionSerializer.Meta attribute) (neuroglancer.serializers.UrlSerializer.Meta attribute)

find_closest_neighbor() (in module brain.forms) formfield_for_foreignkey() (brain.admin.AtlasAdminModel method) formfield_overrides (neuroglancer.admin.UrlModelAdmin attribute) formset (brain.admin.TifInline attribute)

G

get() (brain.views.AnimalDetail method) (brain.views.AnimalList method) (brain.views.ScanResolution method) (neuroglancer.views.ContoursToVolume method) (neuroglancer.views.GetCellTypes method) (neuroglancer.views.GetCOM method) (neuroglancer.views.GetComList method) (neuroglancer.views.GetMarkedCell method) (neuroglancer.views.GetMarkedCellList method) (neuroglancer.views.GetPolygonList method) (neuroglancer.views.GetVolume method) (neuroglancer.views.LandmarkList method) (neuroglancer.views.Rotation method) (neuroglancer.views.Rotations method) (neuroglancer.views.SaveAnnotation method) get_animal() (neuroglancer.admin.ArchiveSetAdmin method) get_annotation_dict() (in module neuroglancer.atlas) get_annotation_type() (neuroglancer.admin.ArchiveSetAdmin method) get_archive() (neuroglancer.annotation_manager.AnnotationManager method) get_fields() (brain.admin.SlideAdmin method) get_formset() (brain.admin.TifInline method)

get_name() (neuroglancer.admin.ArchiveSetAdmin method) get_object() (brain.views.AnimalDetail method) get_points_in_session() (in module neuroglancer.admin) get_queryset() (brain.admin.SectionAdmin method) (brain.admin.TifInline method) (neuroglancer.admin.AnnotationSessionAdmin method) (neuroglancer.admin.ArchiveSetAdmin method) (neuroglancer.admin.PointsAdmin method) (neuroglancer.admin.StructureComAdmin method) get_scales() (in module neuroglancer.atlas) get_session() (neuroglancer.annotation_manager.AnnotationManager method) get_urls() (neuroglancer.admin.AnnotationSessionAdmin method) (neuroglancer.admin.PointsAdmin method) (neuroglancer.admin.StructureComAdmin method) GetCellTypes (class in neuroglancer.views) GetCOM (class in neuroglancer.views) GetComList (class in neuroglancer.views) GetMarkedCell (class in neuroglancer.views) GetMarkedCellList (class in neuroglancer.views) GetPolygonList (class in neuroglancer.views) GetVolume (class in neuroglancer.views)

H

has_add_permission() (brain.admin.LogEntryAdmin method) (brain.admin.SectionAdmin method) (brain.admin.SlideAdmin method) (brain.admin.SlideCziToTifAdmin method) (brain.admin.TifInline method) (neuroglancer.admin.ArchiveSetAdmin method) (neuroglancer.admin.CompletedTaskAdmin method) (neuroglancer.admin.MarkedCellWorkflowAdmin method) (neuroglancer.admin.PointsAdmin method) (neuroglancer.admin.TaskAdmin method) (neuroglancer.admin.UrlModelAdmin method) has_change_permission() (brain.admin.LogEntryAdmin method) (brain.admin.SectionAdmin method) (brain.admin.TifInline method) (neuroglancer.admin.ArchiveSetAdmin method) (neuroglancer.admin.CompletedTaskAdmin method) (neuroglancer.admin.MarkedCellWorkflowAdmin method) (neuroglancer.admin.PointsAdmin method)

has_delete_permission() (brain.admin.LogEntryAdmin method) (brain.admin.SectionAdmin method) (brain.admin.SlideAdmin method) (brain.admin.SlideCziToTifAdmin method) (neuroglancer.admin.ArchiveSetAdmin method) (neuroglancer.admin.MarkedCellWorkflowAdmin method) (neuroglancer.admin.PointsAdmin method) has_view_permission() (brain.admin.LogEntryAdmin method) histogram() (brain.models.Animal method) (brain.models.Section method) Histology (class in brain.models) Histology.DoesNotExist Histology.MultipleObjectsReturned HistologyAdmin (class in brain.admin)

I

image_list() (in module brain.views) image_tag() (brain.models.Section method) Injection (class in brain.models) Injection.DoesNotExist Injection.MultipleObjectsReturned injection_comments() (brain.admin.InjectionVirusAdmin method)

InjectionAdmin (class in brain.admin) InjectionVirus (class in brain.models) InjectionVirus.DoesNotExist InjectionVirus.MultipleObjectsReturned InjectionVirusAdmin (class in brain.admin) is_active() (brain.admin.AtlasAdminModel method) is_structure_com() (neuroglancer.annotation_manager.AnnotationManager method)

L

label() (neuroglancer.admin.AnnotationSessionAdmin method) label_from_instance() (brain.forms.AnimalChoiceField method) LandmarkList (class in neuroglancer.views) list_display (neuroglancer.admin.AnnotationSessionAdmin attribute) (neuroglancer.admin.ArchiveSetAdmin attribute) (neuroglancer.admin.BrainRegionAdmin attribute) (neuroglancer.admin.CellTypeAdmin attribute) (neuroglancer.admin.CompletedTaskAdmin attribute) (neuroglancer.admin.PointsAdmin attribute) (neuroglancer.admin.StructureComAdmin attribute) (neuroglancer.admin.TaskAdmin attribute) (neuroglancer.admin.UrlModelAdmin attribute)

list_display_links (brain.admin.SectionAdmin attribute) list_filter (neuroglancer.admin.AnnotationSessionAdmin attribute) (neuroglancer.admin.ArchiveSetAdmin attribute) (neuroglancer.admin.BrainRegionAdmin attribute) (neuroglancer.admin.CellTypeAdmin attribute) (neuroglancer.admin.CompletedTaskAdmin attribute) (neuroglancer.admin.MarkedCellWorkflowAdmin attribute) (neuroglancer.admin.PointsAdmin attribute) (neuroglancer.admin.UrlModelAdmin attribute) LogEntryAdmin (class in brain.admin)

M

make_active() (in module neuroglancer.admin) make_inactive() (in module neuroglancer.admin) marked_cells() (neuroglancer.admin.MarkedCellWorkflowAdmin method) MarkedCell (class in neuroglancer.models) MarkedCell.DoesNotExist MarkedCell.MultipleObjectsReturned MarkedCell.SourceChoices (class in neuroglancer.models) MarkedCellListSerializer (class in neuroglancer.serializers) MarkedCellWorkflow (class in neuroglancer.models) MarkedCellWorkflow.DoesNotExist MarkedCellWorkflow.MultipleObjectsReturned MarkedCellWorkflowAdmin (class in neuroglancer.admin) max_scene() (brain.models.SlideCziToTif method) media (brain.forms.AnimalForm property) (neuroglancer.admin.AnnotationSessionAdmin property) (neuroglancer.admin.ArchiveSetAdmin property) (neuroglancer.admin.BrainRegionAdmin property) (neuroglancer.admin.CellTypeAdmin property) (neuroglancer.admin.CompletedTaskAdmin property) (neuroglancer.admin.MarkedCellWorkflowAdmin property) (neuroglancer.admin.PointsAdmin property) (neuroglancer.admin.StructureComAdmin property) (neuroglancer.admin.TaskAdmin property) (neuroglancer.admin.UrlModelAdmin property)

midsection() (neuroglancer.models.BrainShape method) model (brain.admin.TifInline attribute) (neuroglancer.serializers.BrainRegionSerializer.Meta attribute) (neuroglancer.serializers.UrlSerializer.Meta attribute) module brain.admin brain.forms brain.models brain.serializers brain.views neuroglancer.admin neuroglancer.annotation_manager neuroglancer.atlas neuroglancer.models neuroglancer.serializers neuroglancer.tasks neuroglancer.tests neuroglancer.views

N

neuroglancer.admin module neuroglancer.annotation_manager module neuroglancer.atlas module neuroglancer.models module

neuroglancer.serializers module neuroglancer.tasks module neuroglancer.tests module neuroglancer.views module nobackground_archive_and_insert_annotations() (in module neuroglancer.tasks)

O

open_multiuser() (neuroglancer.admin.UrlModelAdmin method) open_neuroglancer() (neuroglancer.admin.AnnotationSessionAdmin method) (neuroglancer.admin.UrlModelAdmin method) ordering (neuroglancer.admin.AnnotationSessionAdmin attribute) (neuroglancer.admin.ArchiveSetAdmin attribute) (neuroglancer.admin.BrainRegionAdmin attribute) (neuroglancer.admin.CellTypeAdmin attribute) (neuroglancer.admin.PointsAdmin attribute) (neuroglancer.admin.StructureComAdmin attribute) (neuroglancer.admin.UrlModelAdmin attribute) (neuroglancer.serializers.UrlSerializer.Meta attribute)

OrganicLabel (class in brain.models) OrganicLabel.DoesNotExist OrganicLabel.MultipleObjectsReturned OrganicLabelAdmin (class in brain.admin)

P

permission_classes (neuroglancer.views.UrlViewSet attribute) Points (class in neuroglancer.models) Points.DoesNotExist Points.MultipleObjectsReturned PointsAdmin (class in neuroglancer.admin) PolygonListSerializer (class in neuroglancer.serializers) PolygonSequence (class in neuroglancer.models)

PolygonSequence.DoesNotExist PolygonSequence.MultipleObjectsReturned PolygonSequence.SourceChoices (class in neuroglancer.models) PolygonSerializer (class in neuroglancer.serializers) prep_id() (brain.admin.InjectionVirusAdmin method) (brain.admin.SlideAdmin method) pretty_url() (neuroglancer.admin.UrlModelAdmin method)

Q

queryset (neuroglancer.views.UrlViewSet attribute)

R

readonly_fields (neuroglancer.admin.BrainRegionAdmin attribute) (neuroglancer.admin.CellTypeAdmin attribute) (neuroglancer.admin.PointsAdmin attribute) (neuroglancer.admin.UrlModelAdmin attribute) remove_scene() (in module brain.forms) repeat_scene() (in module brain.forms)

response_change() (brain.admin.SlideAdmin method) restore_annotations() (in module neuroglancer.tasks) restore_archive() (in module neuroglancer.admin) Rotation (class in neuroglancer.views) Rotations (class in neuroglancer.views) RotationSerializer (class in neuroglancer.serializers)

S

save_existing() (brain.forms.TifInlineFormset method) save_model() (brain.admin.SlideAdmin method) save_neuroglancer_state() (neuroglancer.serializers.UrlSerializer method) save_slide_model() (in module brain.forms) SaveAnnotation (class in neuroglancer.views) ScanResolution (class in brain.views) ScanRun (class in brain.models) ScanRun.DoesNotExist ScanRun.MultipleObjectsReturned ScanRunAdmin (class in brain.admin) scene() (brain.models.Section method) scene_count() (brain.admin.SlideAdmin method) scene_image() (brain.admin.TifInline method) scene_reorder() (in module brain.forms) search_fields (neuroglancer.admin.AnnotationSessionAdmin attribute) (neuroglancer.admin.ArchiveSetAdmin attribute) (neuroglancer.admin.BrainRegionAdmin attribute) (neuroglancer.admin.CellTypeAdmin attribute) (neuroglancer.admin.MarkedCellWorkflowAdmin attribute) (neuroglancer.admin.PointsAdmin attribute) (neuroglancer.admin.StructureComAdmin attribute) (neuroglancer.admin.TaskAdmin attribute) (neuroglancer.admin.UrlModelAdmin attribute) Section (class in brain.models) Section.DoesNotExist Section.MultipleObjectsReturned

section_image() (brain.admin.TifInline method) section_number() (brain.admin.SectionAdmin method) SectionAdmin (class in brain.admin) SectionAdmin.Media (class in brain.admin) serializer_class (neuroglancer.views.UrlViewSet attribute) set_current_layer() (neuroglancer.annotation_manager.AnnotationManager method) set_end() (in module brain.forms) set_scene_active_inactive() (in module brain.forms) setUp() (neuroglancer.tests.TestSetUp method) show_com() (neuroglancer.admin.StructureComAdmin method) show_points() (neuroglancer.admin.AnnotationSessionAdmin method) (neuroglancer.admin.PointsAdmin method) Slide (class in brain.models) slide() (brain.models.Section method) Slide.DoesNotExist Slide.MultipleObjectsReturned SlideAdmin (class in brain.admin) SlideCziToTif (class in brain.models) SlideCziToTif.DoesNotExist SlideCziToTif.MultipleObjectsReturned SlideCziToTifAdmin (class in brain.admin) StructureCom (class in neuroglancer.models) StructureCom.DoesNotExist StructureCom.MultipleObjectsReturned StructureCom.SourceChoices (class in neuroglancer.models) StructureComAdmin (class in neuroglancer.admin)

T

TaskAdmin (class in neuroglancer.admin) test_get_com() (neuroglancer.tests.TestAnnotations method) test_get_com_list() (neuroglancer.tests.TestAnnotations method) test_get_landmark_list() (neuroglancer.tests.TestNeuroglancer method) test_get_marked_cell() (neuroglancer.tests.TestAnnotations method) test_get_marked_cell_list() (neuroglancer.tests.TestAnnotations method) test_get_rotation() (neuroglancer.tests.TestTransformation method) test_get_rotation_inverse() (neuroglancer.tests.TestTransformation method) test_get_rotation_inverse_rescale() (neuroglancer.tests.TestTransformation method) test_get_rotation_rescale() (neuroglancer.tests.TestTransformation method) test_get_volume() (neuroglancer.tests.TestAnnotations method) test_get_volume_list() (neuroglancer.tests.TestAnnotations method)

test_neuroglancer_url() (neuroglancer.tests.TestNeuroglancer method) test_rotation_list() (neuroglancer.tests.TestTransformation method) test_rotation_url_with_bad_animal() (neuroglancer.tests.TestTransformation method) test_save_annotations() (neuroglancer.tests.TestNeuroglancer method) test_save_annotations_377() (neuroglancer.tests.TestNeuroglancer method) TestAnnotations (class in neuroglancer.tests) TestNeuroglancer (class in neuroglancer.tests) TestSetUp (class in neuroglancer.tests) TestTransformation (class in neuroglancer.tests) tif() (brain.models.Section method) TifInline (class in brain.admin) TifInlineFormset (class in brain.forms)

U

umeyama() (in module neuroglancer.atlas) update() (neuroglancer.serializers.UrlSerializer method) UrlModel (class in neuroglancer.models) UrlModel.DoesNotExist

UrlModel.MultipleObjectsReturned UrlModelAdmin (class in neuroglancer.admin) UrlSerializer (class in neuroglancer.serializers) UrlSerializer.Meta (class in neuroglancer.serializers) UrlViewSet (class in neuroglancer.views)

V

view_coms() (neuroglancer.admin.StructureComAdmin method) view_points_3Dgraph() (neuroglancer.admin.PointsAdmin method) view_points_data() (neuroglancer.admin.PointsAdmin method) view_points_in_session() (neuroglancer.admin.AnnotationSessionAdmin method)

Virus (class in brain.models) Virus.DoesNotExist Virus.MultipleObjectsReturned virus_name() (brain.admin.InjectionVirusAdmin method) VirusAdmin (class in brain.admin)