Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Wiki Markup
h1. DOWNLOADING 3-D EXPRESSION GRID DATA

...

Table of Contents
minLevel2
maxLevel3
stylenone
classtoc-style

...



{toc:style=none|minLevel=2|maxLevel=3|class=toc-style}

!voxel_level_expression.png|width=32! Download 3-D expression grid data packaged into a compressed archive file (.zip).

...

Prototype

No Format


h2. Prototype

{noformat}
http://api.brain-map.org/grid_data/download_file/[SectionDataSet.id]&include=[volumes]

Examples

Download the intensity and density volumes for SectionDataSet 69816930:

No Format
&resolution=[resolution]
{noformat}

h2. Examples

Download the intensity and density volumes for SectionDataSet 69816930:

{noformat}
http://api.brain-map.org/grid_data/download_file/69816930?include=intensity,density
{noformat}

Download the

...

 100um density volume for the Mouse Connectivity Projection experiment 183282970:

...



{noformat
}
http://api.brain-map.org/grid_data/download_file/183282970
{noformat}
Download the 25um density volume for the Mouse Connectivity Projection experiment 183282970:

{noformat}
http://api.brain-map.org/grid_data/download_file/183282970?resolution=25
{noformat}
Download the energy volume for the Mouse Brain Atlas' coronal Adora2a experiment.

...



    First, search for relevant experiments' IDs (SectionDataSets):

...



{noformat
}
http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eq'false'],products[abbreviation$eq'Mouse'],plane_of_section[name$eq'coronal'],genes[acronym$eq'Adora2a']

...

{noformat}
    Then, download the energy volume for each of the experiments' IDs:

...



{noformat
}
http://api.brain-map.org/grid_data/download/72109410

Parameters

filename

Integer

ID of the desired SectionDataSet.

volumes

Array (optional)

Explicitly list the desired volumes as a comma-separated list. Valid volumes are energy, intensity and density. An additional volume of injection is available for Projection SectionDataSets. 

Response

...

?include=energy
{noformat}

h2. Parameters

| filename | Integer | ID of the desired SectionDataSet. |
| volumes | Array (optional) | Explicitly list the desired volumes as a comma-separated list. Valid volumes are energy, intensity and density. An additional volume of injection is available for projection SectionDataSets.  |
| resolution | Integer | For projection data, available resolutions are 10, 25, 50, and 150 (in microns). For adult mouse gene expression SectionDataSets, only 200um resolution data is available and will be returned regardless of the input value. |

h2. Response

Zip file (.zip) containing a folder filled with the default files (data_set.xml, energy.mhd, energy.raw) or the requested data volumes.

...

data_set.xml

...

XML file with details regarding the specimen and images that is only returned if the volumes parameter is null.

...

energy.mhd

...

A simple text header file in MetaImage format describing the volume. This file is returned by default if the volumes parameter is null.

...

energy.raw

...



| energy_{resolution}.nrrd | A simple text header file in MetaImage format describing the volume. This file is returned by default if the volumes parameter is null. |
| density_{resolution}.nrrd | A raw uncompressed float (32-bit) little-endian volume representing average expression energy per voxel. A value of "-1" represents no data. This file is returned by default if the volumes parameter is null.

...

density.mhd

...

A simple text header file in MetaImage format describing the volume.

...

density.raw

...

 |
| intensity_{resolution}.nrrd | A simple text header file in MetaImage format describing the volume. |
| injection_{resolution}.nrrd | A raw uncompressed float (32-bit) little-endian volume representing average expression density per voxel. A value of "-1" represents no data.

...

intensity.mhd

...

A simple text header file in MetaImage format describing the volume.

...

intensity.raw

...

A raw uncompressed float (32-bit) little-endian volume representing average expression intensity per voxel. A value of "-1" represents no data.

...

injection.mhd

...

A simple text header file in MetaImage format describing the volume.

...

injection.raw

...

A raw uncompressed float (32-bit) little-endian volume representing the proportion of pixels within each voxel that were within the manually annotated injection site.

 |