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Application Programming Interface
The application programming interface enables programmatic access to the data presented in the http://analysis.marmosetbrain.org interface. You can use this API to retrieve various kinds of datasets for the purpose of your research.
Please note that the data is distributed under the terms of the CC BY-SA 4.0 licence. When using the data, please acknowledge the following articles:
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Majka P., Bai S., Bakola S., Bednarek S., Chan J.C., Jermakow N., Passarelli L., Reser D.H., Theodoni P., Worthy K.H., Wang X-J., Wójcik D.K., Mitra P.P. & Rosa M.G.P. (2020). Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey. Nature Communications. http://doi.org/10.1038/s41467-020-14858-0.
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Majka, P., Chaplin, T. A., Yu, H.-H., Tolpygo, A., Mitra, P. P., Wójcik, D. K., & Rosa, M. G. P. (2016). Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. Journal of Comparative Neurology, 524(11), 2161–2181. http://doi.org/10.1002/cne.24023.
- List Injections
- List Cases
- List Tracers
- List Areas
- List Areas (In flat structure)
- Retrograde connectivity pattern per area
- Retrograde connectivity pattern per injection
- Retrieve Cells
- Download tracer data as 3D volume
Lists all injections published on the http://marmosetbrain.org portal.
Property | Data Type | Description |
---|---|---|
id |
String | Unique identifier of the injection in the system |
case_id |
String | Unique identifier of the case studied |
display_name |
String | Human-readable identifier of the case without unnecessary underlying technicalities |
area |
String | The target area of the injection |
section |
String | The section which the injection site is at |
tracer |
String | The tracer used in this injection |
A-P |
Float | Rostrocaudal stereotaxic coordinate (mm): Positive values are caudal to the interaural line. Negative values are rostral to the interaural line |
M-L |
Float | Mediolateral stereotaxic coordinate (mm): The values increase towards the lateral direction |
D-V |
Float | Dorsoventral stereotaxic coordinate (mm): Values increase towards the dorsal direction from the interaural line |
url_to_highres_viewer |
String | A URL link to the high-resolution viewer to investigate the cells and histology of the injection |
url_to_flatmap_image |
String | A URL link pointing to the Flatmap image of this injection |
memo |
String | Expert anatomist comment aimed at helping detailed interpretation the injection |
http://www.marmosetbrain.org/api/v1/injections
{
"status": "success",
"timestamp": 1516081347,
injections: [
{
memo: "DY injection in the caudal part of area 8b. Pattern of label is similar to FB injection suggesting no involvement of cortex caudal to 8b (area 6M).",
url_to_highres_viewer: "http://www.marmosetbrain.org/goto/CJ74/r17b/13.145892/6.221157/3",
M-L: "0.19",
A-P: "13.28",
url_to_flatmap_image: "http://flatmap.marmosetbrain.org/flatmap/CJ74/DY.png",
id: "CJ74-DY",
display_name: "CJ74-DY",
section: "r17b",
tracer: "DY",
case_id: "CJ74",
D-V: "14.98",
area: "A8b"
},
...
],
"total_injections": 141,
}
Lists all cases (animals).
Property | Data Type | Description |
---|---|---|
id |
String | Unique identifier of the case in the system |
sex |
String | The sex of the animal studied |
date_of_birth |
String | The animal's date of birth |
injection_date |
Float | The date of injection performed |
perfusion_date |
String | The date of perfusion of the brain |
survival_days |
Integer | The number of days between surgery and brain is extracted |
sectioning_plane |
String | The sectioning plane of the brain. |
weight |
Integer | The weight of the animal at the time of surgery (in grams) |
memo |
String | Expert anatomist comment on the animal and the experiment |
http://www.marmosetbrain.org/api/v1/cases
{
status: "success",
timestamp: 1516081172,
cases: [
{
id: "CJ122",
sex: "M"
date_of_birth: "2008-07-23",
injection_date: "2011-06-01",
perfusion_date: "2011-06-15",
survival_days: 14,
sectioning_plane: "coronal",
weight: 318,
memo: "This animal had 4 injections in temporal cortex.",
},
...
],
total_cases: 54
}
Lists retrograde fluorescent traces used in the injections.
Property | Data Type | Description |
---|---|---|
id |
String | The unique id for the tracer used in the website |
name |
String | The human-readable name of the tracer |
description |
String | More verbose description for the tracer |
color_code |
String | The HEX color code for the tracer |
comment |
String | Any comment for this tracer |
http://www.marmosetbrain.org/api/v1/tracers
{
status: "success",
timestamp: 1516861357,
total_tracers: 6,
tracers: [
{
comment: null,
description: "Diamidino Yellow (DY)",
name: "Diamidino yellow",
id: "DY",
color_code: "#F9EBAA"
},
...
]
}
Lists cortical areas in a nested dictionary format.
Property | Data Type | Description |
---|---|---|
id |
Integer | The unique identifier of the cortical area |
is_leaf |
Boolean | Indicates if an area has any child areas (is_leaf is true ) or if it has no child areas defined (is_leaf is false ) |
name |
String | The name of the area |
abbrev |
String | The unique reference code in the system for the area |
human_readable_abbrev |
String | Human-readable abbreviation of the area. The code aligns with the Atlas name |
color_code |
String | The HEX color code for the area. The color is used throughout the website |
nodes |
Object | The child nodes of the area if it is not a leaf. Each item is keyed by the area's abbrev |
http://www.marmosetbrain.org/api/v1/areas
{
status: "success",
timestamp: 1516083344,
areas: {
is_leaf: false,
human_readable_abbrev: "ProCeph",
color_code: "#00FF28",
abbrev: "ProCeph",
id: 102,
name: "Prosencephalon",
nodes: [
{
is_leaf: false,
human_readable_abbrev: "TelCeph",
color_code: "#0EFF00",
abbrev: "TelCeph",
nodes: [
...
]
id: 125,
name: "Telencephalon",
},
...
]
}
}
Lists areas in flattened object format. The key will be the abbrev identifier of the area in the system. Only leaf nodes are listed. If a full list contains parent nodes is desired, please use http://www.marmosetbrain.org/api/v1/areas
Property | Data Type | Description |
---|---|---|
id |
Integer | The unique identifier of the cortical area |
name |
String | The name of the area |
abbrev |
String | The unique reference code in the system for the area |
human_readable_abbrev |
String | Human-readable abbreviation of the area. The code aligns with the Atlas name |
color_code |
String | The HEX color code for the area. The color is used throughout the website |
http://www.marmosetbrain.org/api/v1/areas/flat
{
status: "success",
timestamp: 1516083344,
areas: {
PGM: {
abbrev: "PGM",
color_code: "#DFD600",
human_readable_abbrev: "PGM",
id: 92,
name: "Parietal area pg, medial part (cortex)"
},
...
}
}
Returns retrograde connectivity pattern for cortical areas.
The connectivity pattern is based on all injections into a specific area. For per injection connectivity profile, use the retrograde connectivity pattern per injection
request.
If an optional area parameter is provided, only the data related to that target area is returned. Otherwise, the full connectivity dataset is returned.
The returned data is either JSON or CSV specified by format parameter.
The column definition is contained in the _comments
attribute in JSON or as the comment in CSV.
Property | Description |
---|---|
format |
The return format of the data, default to JSON. Possible values JSON, CSV |
area |
Limit the result to interested target area, possible values: |
Property | Data Type | Description |
---|---|---|
target |
String | The target area of the connection |
source |
String | The source area of the injection |
flne |
Float | Fraction of extrinsic labelled neurons |
log10_flne |
Float | The strength of the connection expressed as a decimal logarithm of the fraction of extrinsic labelled neurons |
http://www.marmosetbrain.org/api/v1/flne_areas?area=V1 http://www.marmosetbrain.org/api/v1/flne_areas
{
status: "success",
timestamp: 1516079479,
total_areas: 3248,
headers: [
"target",
"source",
"flne",
"log10_flne"
],
_comments: "# This file contains FLNe values for all areas # Columns description: # 1) Target: area receiving the projection, # 2) Source: area sending the projection, # 3) FLNe: fraction of extrinsic labelled neurons, # 4) log10_flne: log10(FLNe). # timestamp (UTC): 2018-01-16 05:11:19 # # This dataset has been downloaded from the # Marmoset Brain Connectivity Atlas # http://www.marmosetbrain.org/ # # The data is released under the terms of CC BY 4.0 license # (https://creativecommons.org/licenses/by/4.0/). # Please follow the citation policy: # http://www.marmosetbrain.org/ # ",
areas: [
[
"OPt",
"MST",
0.177431097244,
-0.7509702617427246
],
...
]
}
Lists the retrograde connectivity pattern for a selected injection.
Property | Description |
---|---|
injection_id (Required) |
Unique identifier of the injection in the system. |
format |
Specify the return format of the result, possible values JSON, CSV |
Property | Data Type | Description |
---|---|---|
case_id |
String | Unique identifier of the case studied |
tracer_id |
String | Unique identifier of tracer used in the injection |
target |
String | The target area of the connection |
source |
String | The source area of the injection |
cell_count |
Integer | The actual number of labelled cells found in the source area |
flne |
Float | Fraction of extrinsic labelled neurons |
log10_flne |
Float | Decimal logarithm of the fraction of extrinsic labelled neurons |
http://www.marmosetbrain.org/api/v1/flne_injections?injection_id=CJ173-DY
{
status: "success",
timestamp: 1516079479,
total_areas: 27,
headers: [
"case_id",
"tracer_id",
"target",
"source",
"cell_count",
"flne",
"log10_flne"
],
_comments: "# This file contains a FLNe values and cell count # for an injection into A4ab in the animal CJ173 # using the DY tracer # Columns description: # 1) Case_id: animal identifier, # 2) Tracer_id: tracer type, # 3) Target: area receiving the projection, # 4) Source: area sending the projection, # 5) Cell_count: the actual number of labelled # cells found in the source area, # 6) FLNe: fraction of extrinsic labelled neurons, # 7) log10_flne: log10(FLNe). # timestamp (UTC): 2018-01-16 06:00:04 # # This dataset has been downloaded from the # Marmoset Brain Connectivity Atlas # http://www.marmosetbrain.org/ # # The data is released under the terms of CC BY 4.0 license # (https://creativecommons.org/licenses/by/4.0/). # Please follow the citation policy: # http://www.marmosetbrain.org/ # ",
areas: [
[
"CJ173",
"DY",
"A4ab",
"A24d",
1855,
0.264320319179,
-0.5778694499287389
],
...
]
}
Returns detailed information on the individual labelled cells identified in a selected injection.
Property | Description |
---|---|
injection_id (Required) |
Unique identifier of the injection in the system |
format |
The return format of the data, default to JSON. Supported formats including CSV, JSON |
Property | Data Type | Description |
---|---|---|
case_id |
String | Unique identifier of the case in the system |
tracer_id |
String | Unique identifier of the tracer type in the system |
target |
String | Area receiving the projection |
source |
String | Area sending the projection |
M-L |
String | Mediolateral stereotaxic coordinate (mm): The values increase towards the lateral direction |
A-P |
String | Rostrocaudal stereotaxic coordinate (mm): Positive values are caudal to the interaural line. Negative values are rostral to the interaural line |
D-V |
String | Dorsoventral stereotaxic coordinate (mm): Values increase towards the dorsal direction from the interaural line |
http://www.marmosetbrain.org/api/v1/cells?injection_id=CJ173-DY
{
status: "success",
timestamp: 1516081417,
cells: [
[
"CJ173",
"DY",
"A4ab",
"DPal",
"+3.07",
"-8.21",
"+15.49",
-1
],
...
],
headers: [
"case_id",
"tracer_id",
"target",
"source",
"M-L",
"A-P",
"D-V",
"laminar position"
],
"total_cells": 7019,
}
Download zip packaged NIfTI format image of the tracer data.
Property | Description |
---|---|
injection_id (Required) |
Unique identifier of the injection in the system |
http://www.marmosetbrain.org/api/v1/volume_map?injection_id=CJ173-DY
A binary data response containing the zip file of the results in NIfTI format.