Introduciton of Brain Regions

[m-nadji-tehrani]

Definition Brain regions are grouping of one or multiple cortical areas which can provide many benefits including:

• help better organizing brain structures in functional units
• reduces clutter
• makes sharing easier
• provides building blocks that can be assembled together

Properties

• By default, the entire genome is considered a single brain region
• brain regions can be nested and each brain region can contain one or more other brain regions or cortical areas or a combination of both
• Each brain region will have a unique id within the genome
• Each cortical region will have a text label
• Each brain region will have a 2D and 3D coordinate that would help identify it within the 3D Brain Monitor and Circuit Builder
• All 2D and 3D locations are local coordinates in perspective to the parent region.
• The size of each brain region will be dependent on the coordinates of its children

Behaviors Identification:

• Top bar should have a new option for brain regions that would be similar to existing cortical areas list feature.
• All brain regions should be listed with the ability to filter by name
• Selecting a given brain region should open a new tab with the brain region content within
• Similar to cortical areas, there should be an add button to create a new region

Creation dialogue:

• A new Create Brain Region dialogue is needed to facilitate the creation of brain region.
• Brain region creation process should include:
  • Title (required)
  • 3D coordinate (required)
  • Members (required) [user should be able to view a list of existing brain regions and cortical areas and select from the list
  • if there is an existing incomming mapping toward any of the brain region members, that cortical area will be automatically labled as a local IPU
  • if there is an existing mapping that is outgoign from a cortical part of a brain region to a cortical area outside the region then such cortical area will be designated as a local OPU

Deletion:

• cortical regions will be automatically deleted if the last member within is deleted. A deletion which would lead to the deletion of a parent brain region should result in a warning and solicit confirmation from the user
• [P2] a region can be manually deleted:
  1. soft delete: will result in disassociation of all members and re-association of members with the parent region
  2. hard delete: will result in deletion of all its members from genome (Destructive but helpful when a large import needs to be reversed)

Modification:

• With the exception of the brain region id, all other properties should be user editable
• User should be able to drag the title bar of a brain region in CB to change its 2D position
• pop-up toolbox in 3D monitor should include an option to change position. The button should pop-up a vector box that enables user to change its 3D location similarly for cortical areas.
• if a cortical area is deleted it will be automatically removed from the brain region registry
• a new pop-up toolbox button should be added to enable user change the association of a cortical area from one brain region to another by simply selecting a destination brain region from a list

Restrictions:

• region of type "root" is the default that covers the entire genome and cannot be deleted
• cortical areas of type CORE, IPU, and OPU can only be a member of the root brain region

Other considerations

• Genome augmentation aka. amalgamation will import cortical areas and brain regions both

API

FEAGI region registry sample:

{ "brain_regions": { "b_412414124": { "title": "visual pathway", "type": "root", "members": { "___pwr": { "type": "area", "coordinate_2d": [3, 12], "coordinate_3d": [3, 12, 33] }, "_death": { "type": "area", "coordinate_2d": [0, 0], "coordinate_3d": [1, 1, 1] }, "b_252342343243": { "type": "region", "coordinate_2d": [0, 0], "coordinate_3d": [1, 1, 1] } } }, "b_4234234234": { "title": "motor pathway", "type": "child", "members": { "VFWEDF": { "type": "area", "coordinate_2d": [3, 12], "coordinate_3d": [3, 12, 33] }, "VFWED2": { "type": "area", "coordinate_2d": [0, 0], "coordinate_3d": [1, 1, 1] }, "b_252342343245": { "type": "region", "coordinate_2d": [0, 0], "coordinate_3d": [1, 1, 1] } } } } }

[Amir-Rasteg]

looks like a good starting point. Also suggest a function to remove cortical areas from a region

[Amir-Rasteg]

Commenting further discussion

• Regions should support "hints" / "suggested" mappings when connecting an input and output
• I personally strongly suggest allowing user defined labels for these inputs and outputs
• These suggested mappings are part of the region object, not the connectome. They only get added to the connectome when a user makes a connection
• Note -> beware of issues of hints when user connects a region output to an input

[Amir-Rasteg]

(instead of making separate issues, will post here)

v1/region/regions is currently unimplemented v1/region/region is a get request with a body

Currently the input / output structure looks like this: Instead, we should have an array per cortical area with the full mapping details

[Amir-Rasteg]

The input / output structure I suggest can look something like this

{ "inputs": { "iv00_C": { "name": "String_Goes_Here", "mappings": { [ {"morphology_id": "projector", "morphology_scalar": [ 1, 1, 1 ], "postSynapticCurrent_multiplier": 1, "plasticity_flag": false, "plasticity_constant": 1, "ltp_multiplier": 1, "ltd_multiplier": 1 }, ] } } } }

(where mappings is an array of mappings using the same structure seen elsewhere in feagi)

[Amir-Rasteg]

To avoid issues with nested regions, we should separate inputs and outputs to "cortical inputs" and "cortical outputs", and "region inputs" and "region outputs"

[Amir-Rasteg]

current summary call is missing dimension information

[Amir-Rasteg]

summary of missing data points I am running into currently:

• No dimension information in summary endpoint
• No Suggested mappings for inputs or outputs

[Amir-Rasteg]

Critical bug: Not all regions contain a 3d coordinate, only the root

[Amir-Rasteg]

name

change the dict to a list, include the name value within the list dictionary element

[Amir-Rasteg]

more detail for above:

inputs / outputs should not contain IPUs/OPUs ignore the previous suggestion about splitting input/outputs for cortical areas and regions, I can calculate regions locally inputs / outputs should be a flat array with each element being a dictionary with a name property, and a mapping(s) property

[m-nadji-tehrani]

Critical bug: Not all regions contain a 3d coordinate, only the root

Fixed