oursin.atlas.ccf

Allen CCF 3D Models

Functions

load_beryl	Load all beryl areas and set visibility to True
load_cosmos	Load all cosmos areas and set visibility to True
set_alpha	Set transparency of CCF area models.
set_color	Set color of CCF area models.
set_colormap	Set colormap used for CCF area intensity mapping
set_data	Set the data array for each CCF area model
set_data_index	Set the data index for the CCF area models
set_intensity	Set color of CCF area models using colormap.
set_material	Set material of CCF area models.
set_visibility	Set visibility of CCF area models

load_beryl()

Load all beryl areas and set visibility to True

NOTE: One of the load functions OR set_area_visibility must be called before you set the color/alpha/etc of brain regions.

load_cosmos()

Load all cosmos areas and set visibility to True

NOTE: One of the load functions OR set_area_visibility must be called before you set the color/alpha/etc of brain regions.

set_visibility(area_visibilities)

Set visibility of CCF area models

Note: you can append a “-lh” or “-rh” suffix to any area acronym or ID to control the visibility of just one-half of the model. This can be used in all of the set_area_* functions.

Parameters

area_visibilitiesdict {stringbool}

dictionary of area IDs or acronyms and visibility values

Examples

>>> urn.set_visibility({'grey':True})
>>> urn.set_visibility({8:True})
>>> urn.set_visibility({'VISp-l':True})

set_color(area_colors)

Set color of CCF area models.

Parameters

area_colorsdict {string: string}

Keys are area IDs or acronyms, Values are hex colors

Examples

>>> urn.set_color( {'grey':"#FFFFFF"})
>>> urn.set_color({8:"#FFFFFF"})
>>> urn.set_color({"VISp-l":"#00000080"})

set_intensity(area_intensities)

Set color of CCF area models using colormap.

Parameters

area_intensitiesdict {string: float}

keys are area IDs or acronyms, values are hex colors

Examples

>>> urn.set_intensity( {'grey':1.0})
>>> urn.set_intensity({8:1.0})

set_colormap(colormap_name)

Set colormap used for CCF area intensity mapping

Options are

• cool (default, teal 0 -> magenta 1)

• grey (black 0 -> white 1)

• grey-green (grey 0, light 1/255 -> dark 1)

• grey-purple (grey 0, light 1/255 -> dark 1)

• grey-red (grey 0, light 1/255 -> dark 1)

• grey-rainbow (grey 0, rainbow colors from 1/255 -> 1)

Parameters

colormap_namestring

colormap name

set_alpha(area_alpha)

Set transparency of CCF area models.

Parameters

area_alphadict {string: float}

keys are area IDs or acronyms, values are percent transparency

Examples

>>> urn.set_alpha( {'grey':0.5})
>>> urn.set_alpha({8:0.5})

set_material(area_materials)

Set material of CCF area models.

Material options are

• ‘opaque-lit’ or ‘default’

• ‘opaque-unlit’

• ‘transparent-lit’

• ‘transparent-unlit’

Parameters

area_materialsdict {string: string}

keys are area IDs or acronyms, values are material options

set_data(area_data)

Set the data array for each CCF area model

Data arrays work the same as the set_area_intensity() function but are controlled by the area_index value, which can be set in the renderer or through the API.

Parameters

area_datadict {string: float list}

keys area IDs or acronyms, values are a list of floats

set_data_index(area_index)

Set the data index for the CCF area models

Parameters

area_indexint

data index