In [69]:
import json
from allensdk.api.api import Api
from allensdk.api.queries.rma.rma_api import RmaApi
from allensdk.api.queries.connectivity.mouse_connectivity_api import MouseConnectivityApi
rma = RmaApi()
def read_data(parsed_json):
return parsed_json['msg']
def pretty(result):
print(json.dumps(result, indent=2))
Download lists of experiments by injection hemisphere, mouse cre line, and injection structure
Download Pvalb experiments injected in the left hemisphere VISp
In [70]:
# Get the atlas id
def query_atlases(search_pattern):
return rma.build_query_url(rma.model_stage('Atlas',
criteria="[name$il'%s']" % (search_pattern),
only=['id', 'name']))
atlases = o.do_query(query_atlases, read_data, 'mouse*')
pretty(atlases)
[
{
"id": 1,
"name": "Mouse, P56, Coronal"
},
{
"id": 4,
"name": "Mouse Coronal, v1 (2008)"
},
{
"id": 5,
"name": "Mouse Sagittal, v1 (2008)"
},
{
"id": 2,
"name": "Mouse, P56, Sagittal"
}
]
In [71]:
# get the structure
def query_structure(acronym, ontology_id):
return rma.build_query_url(rma.model_stage('Structure',
criteria="[acronym$eq'%s'][ontology_id$eq%d]" % (acronym, ontology_id),
only=['id','name']))
structure = o.do_query(query_structure, read_data, 'VISp', 1)[0]
pretty(structure)
{
"id": 385,
"name": "Primary visual area"
}
In [45]:
def query_hemisphere(name):
return rma.build_query_url(rma.model_stage('Hemisphere', criteria="[name$il'%s']" % (name)))
left_hemisphere_id = o.do_query(query_hemisphere, read_data, 'left')[0]['id']
left_hemisphere_id
Out[45]:
1
In [73]:
mca = MouseConnectivityApi()
experiments = mca.get_experiments(structure['id'])
# TODO: figure out why this didn't work w/ left hemisphere
other_hemisphere_id = 3
# get experiments doesn't take hemisphere into account, so filter the results with a list comprehension
left_hemisphere_experiments = [e for e in experiments
if any([(injection['primary_injection_structure']['hemisphere_id'] == other_hemisphere_id)
for injection in e['specimen']['stereotaxic_injections']])]
pretty(left_hemisphere_experiments)
[
{
"specimen": {
"stereotaxic_injections": [
{
"days_post_injection": 21,
"injection_quality": "1",
"injection_method": "Iontophoresis",
"specimen_id": 267400622,
"sphinx_id": 1925,
"primary_injection_structure_id": 385,
"age_id": 15,
"targeted_injection_structure_id": 385,
"primary_injection_structure": {
"st_level": null,
"graph_id": 1,
"name": "Primary visual area",
"weight": 8690,
"acronym": "VISp",
"parent_structure_id": 669,
"graph_order": 168,
"sphinx_id": 169,
"hemisphere_id": 3,
"safe_name": "Primary visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/385/",
"failed": false,
"depth": 7,
"neuro_name_structure_id_path": null,
"neuro_name_structure_id": null,
"structure_name_facet": 3425643282,
"failed_facet": 734881840,
"id": 385,
"ontology_id": 1,
"atlas_id": 755
},
"structures": [
{
"st_level": null,
"graph_id": 1,
"name": "Primary visual area",
"weight": 8690,
"acronym": "VISp",
"parent_structure_id": 669,
"graph_order": 168,
"sphinx_id": 169,
"hemisphere_id": 3,
"safe_name": "Primary visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/385/",
"failed": false,
"depth": 7,
"neuro_name_structure_id_path": null,
"neuro_name_structure_id": null,
"structure_name_facet": 3425643282,
"failed_facet": 734881840,
"id": 385,
"ontology_id": 1,
"atlas_id": 755
}
],
"id": 267400634
}
],
"structure_id": null,
"sphinx_id": 21790,
"name": "378-1920",
"weight": 9000,
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"rna_integrity_number": null,
"failed_facet": 734881840,
"parent_id": null,
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"donor_id": 267400608,
"parent_x_coord": null,
"ephys_result_id": null,
"is_cell_specimen": null,
"specimen_id_path": "/267400622/",
"is_ish": false,
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},
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"qc_date": "2013-09-05T00:06:02Z",
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"delegate": false,
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"red_channel": "background fluorescence",
"section_thickness": 100.0,
"expression": false,
"id": 277616630,
"plane_of_section_id": 1
},
{
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{
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"injection_quality": "1",
"injection_method": "Iontophoresis",
"specimen_id": 278222408,
"sphinx_id": 5921,
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"age_id": 15,
"targeted_injection_structure_id": 385,
"primary_injection_structure": {
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"graph_id": 1,
"name": "Primary visual area",
"weight": 8690,
"acronym": "VISp",
"parent_structure_id": 669,
"graph_order": 168,
"sphinx_id": 169,
"hemisphere_id": 3,
"safe_name": "Primary visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/385/",
"failed": false,
"depth": 7,
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"neuro_name_structure_id": null,
"structure_name_facet": 3425643282,
"failed_facet": 734881840,
"id": 385,
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"atlas_id": 755
},
"structures": [
{
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"weight": 8690,
"acronym": "VISp",
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"failed": false,
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}
],
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}
],
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"failed_facet": 734881840,
"parent_id": null,
"hemisphere": null,
"donor_id": 287954683,
"parent_x_coord": null,
"ephys_result_id": null,
"is_cell_specimen": null,
"specimen_id_path": "/287954688/",
"is_ish": false,
"id": 287954688,
"external_specimen_name": "123726",
"parent_z_coord": null
},
"name": null,
"weight": 5140,
"rnaseq_design_id": null,
"qc_date": "2014-10-03T22:13:52Z",
"reference_space_id": 9,
"sphinx_id": 110658,
"blue_channel": "background fluorescence",
"failed_facet": 734881840,
"green_channel": "rAAV",
"failed": false,
"storage_directory": "/external/connectivity/prod444/image_series_308879859/",
"delegate": false,
"specimen_id": 287954688,
"red_channel": "background fluorescence",
"section_thickness": 100.0,
"expression": false,
"id": 308879859,
"plane_of_section_id": 1
},
{
"specimen": {
"stereotaxic_injections": [
{
"days_post_injection": 21,
"injection_quality": null,
"injection_method": "Iontophoresis",
"specimen_id": 308011756,
"sphinx_id": 2540,
"primary_injection_structure_id": 385,
"age_id": 298107438,
"targeted_injection_structure_id": 385,
"primary_injection_structure": {
"st_level": null,
"graph_id": 1,
"name": "Primary visual area",
"weight": 8690,
"acronym": "VISp",
"parent_structure_id": 669,
"graph_order": 168,
"sphinx_id": 169,
"hemisphere_id": 3,
"safe_name": "Primary visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/385/",
"failed": false,
"depth": 7,
"neuro_name_structure_id_path": null,
"neuro_name_structure_id": null,
"structure_name_facet": 3425643282,
"failed_facet": 734881840,
"id": 385,
"ontology_id": 1,
"atlas_id": 755
},
"structures": [
{
"st_level": null,
"graph_id": 1,
"name": "Anteromedial visual area",
"weight": 8690,
"acronym": "VISam",
"parent_structure_id": 669,
"graph_order": 154,
"sphinx_id": 155,
"hemisphere_id": 3,
"safe_name": "Anteromedial visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/394/",
"failed": false,
"depth": 7,
"neuro_name_structure_id_path": null,
"neuro_name_structure_id": null,
"structure_name_facet": 1045871632,
"failed_facet": 734881840,
"id": 394,
"ontology_id": 1,
"atlas_id": 756
},
{
"st_level": null,
"graph_id": 1,
"name": "Primary visual area",
"weight": 8690,
"acronym": "VISp",
"parent_structure_id": 669,
"graph_order": 168,
"sphinx_id": 169,
"hemisphere_id": 3,
"safe_name": "Primary visual area",
"color_hex_triplet": "08858C",
"structure_id_path": "/997/8/567/688/695/315/669/385/",
"failed": false,
"depth": 7,
"neuro_name_structure_id_path": null,
"neuro_name_structure_id": null,
"structure_name_facet": 3425643282,
"failed_facet": 734881840,
"id": 385,
"ontology_id": 1,
"atlas_id": 755
}
],
"id": 308011764
}
],
"structure_id": null,
"sphinx_id": 2195,
"name": "C57BL/6-155460",
"weight": 9000,
"tissue_ph": null,
"parent_y_coord": null,
"rna_integrity_number": null,
"failed_facet": 734881840,
"parent_id": null,
"hemisphere": null,
"donor_id": 308011754,
"parent_x_coord": null,
"ephys_result_id": null,
"is_cell_specimen": null,
"specimen_id_path": "/308011756/",
"is_ish": false,
"id": 308011756,
"external_specimen_name": "155460",
"parent_z_coord": null
},
"name": null,
"weight": 5140,
"rnaseq_design_id": null,
"qc_date": "2014-10-07T21:00:51Z",
"reference_space_id": 9,
"sphinx_id": 159352,
"blue_channel": "background fluorescence",
"failed_facet": 734881840,
"green_channel": "rAAV",
"failed": false,
"storage_directory": "/external/connectivity/prod445/image_series_309113907/",
"delegate": false,
"specimen_id": 308011756,
"red_channel": "background fluorescence",
"section_thickness": 100.0,
"expression": false,
"id": 309113907,
"plane_of_section_id": 1
}
]
Download grid data for these experiments at a particular resolution
In [75]:
from allensdk.api.queries.grid_data.grid_data_api import GridDataApi
10, 25, 50, or 100 micron volumes for:
* Projection density
* projection energy
* injection fraction
* Injection density
* Injection energy
* Data mask (mask of valid voxels per experiment)
In [79]:
gda = GridDataApi()
# TODO: show search to get this
section_data_set_id = 183282970
image_list = ['projection_density',
'projection_energy',
'injection_fraction',
'injection_density',
'injection_energy']
resolution = 100 # or 10, 25, 50
# Hmm, this didn't work for an image list of length > 1
for image in image_list:
q = gda.build_projection_grid_download_query(section_data_set_id,
image=[image],
resolution=resolution)
print(q)
# gda.download_projection_grid_data(section_data_set_id,
# image=image,
# resolution=resolution)
# TODO: data mask
http://api.brain-map.org/grid_data/download_file/183282970?image=projection_density&resolution=100
http://api.brain-map.org/grid_data/download_file/183282970?image=projection_energy&resolution=100
http://api.brain-map.org/grid_data/download_file/183282970?image=injection_fraction&resolution=100
http://api.brain-map.org/grid_data/download_file/183282970?image=injection_density&resolution=100
http://api.brain-map.org/grid_data/download_file/183282970?image=injection_energy&resolution=100
http://help.brain-map.org//display/mouseconnectivity/API#API-Expression3DGrids
In [82]:
q = gda.build_expression_grid_download_query(section_data_set_id, include=image_list)
print q
http://api.brain-map.org/grid_data/download/183282970?include=projection_density,projection_energy,injection_fraction,injection_density,injection_energy
Read data (File mode):
Read experiment metadata by injection hemisphere, mouse cre line, and injection structure
“I download a list of all experiments. Which were injected in VISp?”
In [94]:
#http://api.brain-map.org/api/v2/data/query.csv?criteria=
#model::ProjectionStructureUnionize,
#rma::criteria,[is_injection$eq'f'],hemisphere,structure,section_data_set[id$eq183282970](specimen(stereotaxic_injections(primary_injection_structure,stereotaxic_injection_coordinates))),rma::include,section_data_set(specimen(stereotaxic_injections(primary_injection_structure))),
#rma::options[tabular$eq'distinct+specimens.name+as+specimen_name,stereotaxic_injection_coordinates.coordinates_ap,stereotaxic_injection_coordinates.coordinates_dv,stereotaxic_injection_coordinates.coordinates_ml,data_sets.id+as+data_set_id,stereotaxic_injections.primary_injection_structure_id,structures.acronym+as+target_structure,hemispheres.symbol+as+hemisphere,projection_structure_unionizes.is_injection,projection_structure_unionizes.sum_pixels,projection_structure_unionizes.sum_projection_pixels,projection_structure_unionizes.sum_pixel_intensity,projection_structure_unionizes.sum_projection_pixel_intensity,projection_structure_unionizes.projection_density,projection_structure_unionizes.projection_intensity,projection_structure_unionizes.projection_energy,projection_structure_unionizes.volume,projection_structure_unionizes.projection_volume,projection_structure_unionizes.normalized_projection_volume,projection_structure_unionizes.max_voxel_density,projection_structure_unionizes.max_voxel_x,projection_structure_unionizes.max_voxel_y,projection_structure_unionizes.max_voxel_z'][start_row$eq0][num_rows$eq3000]
def build_query(section_data_set_id):
criteria_string = ''.join(["[is_injection$eq'f'],",
"hemisphere,",
"structure,",
"section_data_set[id$eq%d]" % (section_data_set_id),
"(specimen",
"(stereotaxic_injections",
"(primary_injection_structure,stereotaxic_injection_coordinates)",
"))"])
include_string = ''.join(["section_data_set",
"(specimen",
"(stereotaxic_injections",
"(primary_injection_structure)",
"))"])
tabular_list = ['distinct+specimens.name+as+specimen_name',
'stereotaxic_injection_coordinates.coordinates_ap',
'stereotaxic_injection_coordinates.coordinates_dv',
'stereotaxic_injection_coordinates.coordinates_ml',
'data_sets.id+as+data_set_id',
'stereotaxic_injections.primary_injection_structure_id',
'structures.acronym+as+target_structure',
'hemispheres.symbol+as+hemisphere',
'projection_structure_unionizes.is_injection',
'projection_structure_unionizes.sum_pixels',
'projection_structure_unionizes.sum_projection_pixels',
'projection_structure_unionizes.sum_pixel_intensity',
'projection_structure_unionizes.sum_projection_pixel_intensity',
'projection_structure_unionizes.projection_density',
'projection_structure_unionizes.projection_intensity',
'projection_structure_unionizes.projection_energy',
'projection_structure_unionizes.volume',
'projection_structure_unionizes.projection_volume',
'projection_structure_unionizes.normalized_projection_volume',
'projection_structure_unionizes.max_voxel_density',
'projection_structure_unionizes.max_voxel_x',
'projection_structure_unionizes.max_voxel_y',
'projection_structure_unionizes.max_voxel_z']
model_stage = rma.model_stage('ProjectionStructureUnionize',
criteria=criteria_string,
include=include_string,
tabular=["'%s'" % ','.join(tabular_list)], # TODO: better handling of tabular quotes
num_rows='all')
url = rma.build_query_url(model_stage, fmt='csv')
return url
print(build_query(183282970))
http://api.brain-map.org/api/v2/data/query.csv?q=model::ProjectionStructureUnionize,rma::criteria,[is_injection$eq'f'],hemisphere,structure,section_data_set[id$eq183282970](specimen(stereotaxic_injections(primary_injection_structure,stereotaxic_injection_coordinates))),rma::include,section_data_set(specimen(stereotaxic_injections(primary_injection_structure))),rma::options[tabular$eq'distinct+specimens.name+as+specimen_name,stereotaxic_injection_coordinates.coordinates_ap,stereotaxic_injection_coordinates.coordinates_dv,stereotaxic_injection_coordinates.coordinates_ml,data_sets.id+as+data_set_id,stereotaxic_injections.primary_injection_structure_id,structures.acronym+as+target_structure,hemispheres.symbol+as+hemisphere,projection_structure_unionizes.is_injection,projection_structure_unionizes.sum_pixels,projection_structure_unionizes.sum_projection_pixels,projection_structure_unionizes.sum_pixel_intensity,projection_structure_unionizes.sum_projection_pixel_intensity,projection_structure_unionizes.projection_density,projection_structure_unionizes.projection_intensity,projection_structure_unionizes.projection_energy,projection_structure_unionizes.volume,projection_structure_unionizes.projection_volume,projection_structure_unionizes.normalized_projection_volume,projection_structure_unionizes.max_voxel_density,projection_structure_unionizes.max_voxel_x,projection_structure_unionizes.max_voxel_y,projection_structure_unionizes.max_voxel_z'][num_rows$eq'all']
Read experiment grid data for these experiments by type
3D numpy arrays worked pretty well for Friday harbor last yearProcess data:
Mask grid data using the data mask or injection fraction volumes “Give me the projection energy voxels from this experiment that are valid for analysis” “Give me the injection density voxels inside the injection site”Mask grid data arrays by structure “Give me the projection density voxel data for voxels belonging to VISp” This will involve the annotation volume at the correct resolution
http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2015/
In [95]:
resolution=25
q = mca.build_volumetric_data_download_url('annotation/ccf_2015', 'annotation_%d.nrrd' % (resolution))
# mca.download_volumetric_data_download('annotation/ccf_2015', 'annotation_%d.nrrd' % (resolution))
print(q)
http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2015/annotation_25.nrrd
In [ ]:
Content source: wvangeit/AllenSDK
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