CoCoMac
CoCoMac - Macaque macro connectivity at your fingertips
CoCoMac 2nd edition home page
CoCoMac 2nd edition home page
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Axonal Projections
Generate list of axonal projections
Look up axonal projections(s) using QRT, the quick version of ORT.
Look up axonal projections(s) using QRT, the quick version of ORT.
Connectivity Matrix
Generate a connectivity matrix from a list of axonal projections
Generate a connectivity matrix from the output of the Axonal Projections service.
Generate a connectivity matrix from the output of the Axonal Projections service.
Custom SQL Query
CoCoMac Direct SQL Query
Send a parameterized SQL query to the CoCoMac database and retrieve the results in html, plain text or json format.
Send a parameterized SQL query to the CoCoMac database and retrieve the results in html, plain text or json format.
Search wizard
CoCoMac Search Wizard
Multi-step search wizard with smart database parsing.
Multi-step search wizard with smart database parsing.
About
About CoCoMac
A brief history of CoCoMac and an overview of current developments.
A brief history of CoCoMac and an overview of current developments.
Citation policy
CoCoMac Citation Policy
If you use CoCoMac connectivity, cite both CoCoMac and the original tracing studies.
If you use CoCoMac connectivity, cite both CoCoMac and the original tracing studies.
Legacy
Legacy CoCoMac Website
G-node is rebuilding the legacy cocomac.org website.
G-node is rebuilding the legacy cocomac.org website.
Data Entry
Data Entry 2010 (view only)
CoCoMac Data entry (2010 version, view only)
The 2010 CoCoMac data entry system stores all forms entered for a particular study in a data entry table, from which the CoCoMac database can be rebuilt to any desired point in time.
The 2010 CoCoMac data entry system stores all forms entered for a particular study in a data entry table, from which the CoCoMac database can be rebuilt to any desired point in time.
FAQ
Frequently Asked Questions
Guidelines to using the API.
Guidelines to using the API.
Research
QRT
Conflicts
Display conflicting mapping paths
Reads results from Floyd algorithm, and displays conflicts
Reads results from Floyd algorithm, and displays conflicts
Core Conflicts
Analyses core conflicting mapping paths
Reads and analyses core conflicts as saved by the Floyd algorithm executable
Reads and analyses core conflicts as saved by the Floyd algorithm executable
Identity Clusters
Compute clusters of identical regions
Compute identity clusters and display them in JSON format
Compute identity clusters and display them in JSON format
Utilities
Brain Site Lookup
Brain site lookup
Lookup brain site details for a given (list of) regions(s), which can be specified either by numeric ID, text ID, acronym or full name
Lookup brain site details for a given (list of) regions(s), which can be specified either by numeric ID, text ID, acronym or full name
F99
F99: Region overlap
Generate table with region overlap between F99-registered atlases
Given a selected pair of atlases that are registered to the F99 cortical surface, this tool counts the vertices that they have in common and returns the overlap as an absolute number or percentage. Note that the surface area represented by a vertex may vary; this is not taken into account.
Given a selected pair of atlases that are registered to the F99 cortical surface, this tool counts the vertices that they have in common and returns the overlap as an absolute number or percentage. Note that the surface area represented by a vertex may vary; this is not taken into account.
F99: Sulcal depth
Compute average sulcal depths of F99-registered atlas regions
Given a selected atlas that is registered to the F99 cortical surface, this tool counts the average sulcal depth of each atlas region by taking the median/average sulcal depth of its vertices.
Given a selected atlas that is registered to the F99 cortical surface, this tool counts the average sulcal depth of each atlas region by taking the median/average sulcal depth of its vertices.
F99: Surface plotting
Plot CoCoMac statistics on the F99 surface
Returns vertex data to plot CoCoMac statistics on the F99 surface.
Returns vertex data to plot CoCoMac statistics on the F99 surface.
Mapping Chain Lookup
QRT mapping path details
Given a numeric QRT path id (or comma separated list thereof), returns the chain of underlying relation statements
Given a numeric QRT path id (or comma separated list thereof), returns the chain of underlying relation statements
Mapping Paths Lookup
QRT mapping paths
Given a brain site numeric or text id (or comma separated list thereof), returns all associated QRT mapping paths
Given a brain site numeric or text id (or comma separated list thereof), returns all associated QRT mapping paths
Mapping Statement Lookup
Lookup a mapping statement by numeric id
Given a numeric mapping statement id (or comma separated list thereof), returns its details
Given a numeric mapping statement id (or comma separated list thereof), returns its details
Sitelist-From-String
Generate list of brain sites from input string
Generates a list of brain site numeric IDs given a string consisting of a comma separated list of brain maps and/or brain sites
Generates a list of brain site numeric IDs given a string consisting of a comma separated list of brain maps and/or brain sites
Tracer history
History of tracers used in CoCoMac
Historic account of tracer substances used in papers contained in CoCoMac
Historic account of tracer substances used in papers contained in CoCoMac
Admin
QRT
1. prepare
Prepare (re)computation of QRT mapping paths
Creates a number of tab-separated files which contain raw data to enter the QRT mapping paths computations
Creates a number of tab-separated files which contain raw data to enter the QRT mapping paths computations
2. (Re)compute
(Re)compute QRT mapping paths
Calls a C++ routine which recomputes the QRT mapping paths and saves the result to a temporary json file. This may take several minutes.
Calls a C++ routine which recomputes the QRT mapping paths and saves the result to a temporary json file. This may take several minutes.
3. Rinish
Finish (re)computation of QRT mapping paths
Reads the resulting QRT mapping paths from a json file and recreates the table QRT_MappingPaths in the relational database
Reads the resulting QRT mapping paths from a json file and recreates the table QRT_MappingPaths in the relational database
4. Fix conflicts
Generate SQL statements that fix (part of) the QRT mapping conflicts
QRT mapping conflicts are chains of inter-map-relation statements that result in incompatible statements about the topological relation between two brain sites. This routine generates SQL statements to fix some of these.
QRT mapping conflicts are chains of inter-map-relation statements that result in incompatible statements about the topological relation between two brain sites. This routine generates SQL statements to fix some of these.
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