Neurochemical Dynamics Atlas

I built this atlas to examine how different substances may converge on overlapping brain circuits, and how those circuits relate to what a person feels, notices, and does. I want to connect that anatomy and neurochemistry with the cues, personal history, and environment surrounding an experience.

This is an experimental part of my Neural Attunement work. I am bringing published findings together with my own interpretations to make those connections visible, examine the evidence behind them, and identify what still needs to be tested.

Conceptual illustration

Circuit guide

Salience & orienting

What it does

Helps identify what deserves attention and shift resources toward it. That can be an opportunity, a body signal, or a possible problem.

What can engage it?

Unexpected events and information relevant to your current needs or goals can engage these processes.

Everyday example

An alarm interrupts what you are doing and draws your attention.

Illustration, not an individual prediction.

Anatomy involved

The anterior insula and dorsal anterior cingulate are common anchors in salience network models. The colored atlas parcels cover broader territories.

Deep anatomy

Locate a broader cortical approximation

Lipid Architecture

Human tissue measurements can be inspected for individually matched circuit nodes. Circuit membership is inherited from the existing Atlas.

Anterior insula

Dorsal anterior cingulate cortex

Thalamus

Connectivity and Lipid Concordance

No circuit specific concordance result or validated human to mouse crosswalk has been imported. The lipid explorer reports the human study’s individual lipid associations with functional connectivity, including its uncorrected p values. Those associations do not establish causal connectivity.

Salience means relevance, not necessarily danger.

Sources for this explanation

Menon (2011)Large-scale brain networks and psychopathology: a unifying triple network model

Khalsa et al. (2018)Interoception and Mental Health: A Roadmap

Source linked educational synthesis. Cortical regions are broad parcel approximations. Deep shapes come from FreeSurfer template segmentations; circuit assignments are an educational synthesis.

Loading the 3D cortex…

Categorical membership · no activation intensity

Inspect a brain region

Drag to rotate. Use the orientation buttons to see hidden surfaces.

Or choose a region

What is actually mapped?

The finer surface contains 81,924 source vertices. The PET map still has 100 parcel values; a smoother surface does not add measurement detail. The 3D model includes cortical and deep template anatomy. Circuit colors are curated teaching regions mapped to source atlas parcels, not measured activity masks. Several are broad cortical proxies. Deep anatomy comes from FreeSurfer segmentations in the fsaverage coordinate system. Small nuclei that are not segmented are identified as broad parent territories or left unmapped.

Salience & orienting: Atlas salience / ventral attention network. Includes cortical orienting partners; thalamus is shown using the deep segmentation.

The cue sequence highlights explanatory topics. It is authored, not a fitted brain simulator. Circuit relationships combine source findings with authored interpretation. Open a circuit’s evidence to inspect the reasoning.

FreeSurfer anatomy and coordinate method · Anatomy license

human functional parcellation

Schaefer et al. (2018)

Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI

Cerebral Cortex, 2018

Candidate cortical parcellation. Functional parcel boundaries are not synonymous with every anatomical subdivision.

10.1093/cercor/bhx179 ↗

Source identity checked in supplied package. Exact claim review and current correction checks remain pending.

review and proposed model

Menon (2011)

Large-scale brain networks and psychopathology: a unifying triple network model

Trends in Cognitive Sciences, 2011

Proposed relationships among salience, executive and default networks across disorders.

10.1016/j.tics.2011.08.003 ↗

Source identity checked in supplied package. Exact claim review and current correction checks remain pending.