Frequently asked questions
- How does CoCoMac work?
- How to generate a connectivity matrix?
- How to use the API?
- How to get your question answered here?
How does CoCoMac work?
CoCoMac is a database (schema) which contains statements collated from the literature on connectivity in the macaque brain.
It covers literature in which neuronal tract-tracing experiments are described.
In these studies, macaque brains are injected with small amounts of axonal tracer, a substance that must have two properties:
- It must be taken up by neurons and transported either away from the soma (anterogradely) or towards the soma (retrogradely), but not cross any synapses.
- It must label (stain) the neuron or axon terminal so that it can be seen under a microscope where the tracer went.
Based on these experiments, statements can be derived about whether there are direct axonal connections between the brain region where the tracer was injected, and the brain regions that were labeled by the tracer.
These statements, 'brain region A has axons projecting to brain region B', go into the database.
Unfortunately there is one big factor that complicates this matter: the 'where' in the brain.
Besides inter-subject variability, different research groups have different opinions on how to parcellate the brain, use different nomenclatures, and apply different procedures to map a location in the brain to their favorite parcellation.
CoCoMac therefore also needs to know how all the different maps that have been used over time relate to each other.
This is done on the basis of 'mapping statements', found in the literature, that (typically) relate the shape of newly defined areas to older parcellation schemes.
Both the mapping statements and connectivity statements are processed by the 'Objective Relational Transformation' routine, and result in connection statements that apply to a chosen parcellation scheme.
How to generate a connectivity matrix?
To generate a connectivity matrix in CoCoMac, a set of origin and target brainsites must be specified between which the connectivity is to be extracted from the database.
This is done by the Axonal Projections
For example, to get connectivity between the regions in the Felleman and Van Essen atlas (FV91), specify the following:
Axon origin sites: FV91
Axon terminal sites: FV91
Large injections: (include)
Acronym-based mapping: yes
Use SORT: no
Now press [Get axonal projections].
This will result in a new temporary database table that contains the results.
From this table, a connectivity matrix can be generated in two ways:
- Using the link in the result page: "View all results". This is the most flexible method.
- Use the separate service 'Generate Connectivity Matrix. This method is less flexible, but has the advantage that it can be invoked with an URL-query, as used by automated scripts.
Once you have used the link "View all results", you first get a long list of axonal projection results. At the top you see a button (Connectivity Matrix) which generates the matrix from the loaded results. NOTE: Make sure that all results are loaded, as indicated in the table header. For example, if it says '100 of 22766 results', you will get a very incomplete connectivity matrix. The resulting connectivity matrix is interactive, you can click on a cell to see which 'pieces of evidence' contributed to it.
How to use the API?
The CoCoMac API consists of a set of four services:
- The Axonal Projections service
- The Connectivity Matrix service
- The Custom SQL Query service
- The CoCoMac Search Wizard service
Each of these services is self-documenting to a large extent.
After submitting a query through the user-interface in the browser,
a URL appears that contains a direct link to the query results.
This URL can be used and adapted by automated scripts.
For example, the Axonal Projections query detailed in the FAQ "How to generate a connectivity matrix?" resulted in this direct URL:
How to get your question answered here?
Send email to Rembrandt Bakker