AIDAmri Version 1.0

ARA/AllenBrainAPI-master/DownloadImageSeries.m

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+function DownloadImageSeries(outdir, expid, varargin)
+% download Allen sample brain using the Allen API
+%
+% function DownloadImageSeries(outdir, expid, varargin)
+%
+% 
+% Inputs [required]
+% outdir - where to put the JPEGs
+% expid  - [numerical scalar] experiment ID assigned by Allen
+%
+% Inputs [optional]
+% 'downsample' sets how many times the image will be downsampled and scaled down, 
+%   e.g. downsample=3 means the image will be 1/2^3 = 1/8 of original size. 
+% 'range' specifies the range of 16 bit RGB values that will be mapped onto 8 bit
+%
+%
+% Example
+% - Pull in a nicely downsampled version of experiment ID 479701339 into the current directory:
+% >> DownloadImageSeries(pwd,479701339,'downsample',4)
+%
+%
+% PZ
+
+
+params = inputParser;
+params.addParamValue('range', '0,2500,0,2500,0,4095', @ischar);
+params.addParamValue('downsample', 2, @isnumeric);
+params.parse(varargin{:});
+
+% download XML data for experiment
+exp_url = ['http://api.brain-map.org/api/v2/data/SectionDataSet/' ...
+    num2str(expid) '.xml?include=section_images'];
+disp(['Accessing ',exp_url]);
+doc = xmlread(exp_url);
+
+% select the image IDs for all images
+list = doc.getElementsByTagName('section-image');
+
+nImages = list.getLength;
+
+% cycle through images, zero-indexed
+for ind = 0:nImages-1
+    thisImage = list.item(ind);
+    imageid = thisImage.getElementsByTagName('id');
+    % number of the brain section (they aren't in order for some reason)
+    sectionnum = thisImage.getElementsByTagName('section-number');
+
+    query = ['http://api.brain-map.org/api/v2/section_image_download/' ...
+        char(imageid.item(0).getFirstChild.getData) ...
+        '?range=' params.Results.range...
+        '&downsample=' num2str(params.Results.downsample)];
+    disp([ num2str(ind+1) ' of ' num2str(nImages) ': ' query]);
+
+    try
+        urlwrite(query,...
+            [ outdir filesep ...
+            char(sectionnum.item(0).getFirstChild.getData) '.jpg']);
+    catch
+        disp(['Error getting image from ',query]);
+    end
+end

ARA/AllenBrainAPI-master/README.md

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+# README #
+
+Tools for accessing the Allen Atlas API from MATLAB. 
+e.g. downloading images, projection data, searching for particular experiments, etc. 
+Functionality isn't complete right now and is a bit rough in places, but everything works and the functions should provide a good template for showing you how to add functionality. 
+For more details see the [Allen API documentation](http://help.brain-map.org/display/mouseconnectivity/API). 
+You will need to install [JSONlab](http://ch.mathworks.com/matlabcentral/fileexchange/33381-jsonlab--a-toolbox-to-encode-decode-json-files-in-matlab-octave) for some functions to work. 
+
+
+
+### Examples ###
+
+Get structure list that underlies the Allen Reference Atlas:
+```
+>> S=getAllenStructureList;
+```
+
+
+Keep only the areas that are children of `Cerebellum`:
+```
+>> S=getAllenStructureList('childrenOf','Cerebellum');
+```
+
+### Also see ###
+There are other useful functions too. See:
+
+* DownloadImageSeries.m 
+* findAllenExperiments.m
+* getInjectionIDfromExperiment.m
+* getProjectionDataFromExperiment.m

ARA/AllenBrainAPI-master/acronym2structureID.m

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+function [IDs,ARA_LIST]=acronym2structureID(acronyms,ARA_LIST,quiet)
+% Convert a list of ARA (Allen Reference Atlas) acronyms to a vector of structure IDs
+%
+% function [IDs,ARA_LIST]=acronym2structureID(acronyms,ARA_LIST,quiet)
+%
+% Purpose
+% Each Allen Reference Atlas (ARA) brain area is associated with a unique
+% number (structure ID), a long name and an acronym. This function converts 
+% the acronym to an area structure ID number.
+% 
+%
+% Inputs
+% acronyms - a cell array (if a list) of brain area acronyms or a single string. 
+% ARA_LIST - [optional] the first output of getAllenStructureList
+% quiet - [optional, false by default] if true, do not print any warning messages
+%
+%
+% Outputs
+% IDs - a vector of brain area structure IDs (if more than one acronym was provided)
+% ARA_LIST - the CSV data from getAllenStructureList in the form of a cell array
+%
+%
+% Examples
+%
+% >> acronym2structureID({'VISp','VISal'}) 
+%
+% ans =
+%
+%  1x2 int32 row vector
+%
+%   385   402
+%
+%
+%
+% Rob Campbell
+%
+% See also:
+% getAllenStructureList, structureID2name
+
+
+if isstr(acronyms)
+    acronyms={acronyms};
+end
+
+if nargin<2 || isempty(ARA_LIST)
+    ARA_LIST = getAllenStructureList;
+end
+
+if nargin<3
+    quiet = false;
+end
+
+%loop through and find all the acronyms
+for ii=1:length(acronyms)
+
+    f=strmatch(lower(acronyms{ii}),lower(ARA_LIST.acronym),'exact');
+    if isempty(f)
+        if ~quiet
+            fprintf('%s finds no acronym %s in the atlas\n',mfilename, acronyms{ii})
+        end
+        continue
+    end
+    if length(f)>1
+        if ~quiet
+            error('found more than one ID index')
+        end
+    end
+    IDs(ii) = ARA_LIST.id(f);
+end
+
+

ARA/AllenBrainAPI-master/examples/thalamus.m

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+function thalamus
+% make a projection density plot
+%
+% This is the MATLAB version of the R example found at
+% http://api.brain-map.org/examples/doc/thalamus/thalamus.R.html
+% 
+% We have some more robust MATLAB functions that encapsulate 
+% some operations that were performed in-line in the R example. 
+% These standalone functions are used where appropriate here. 
+%
+%
+% Rob Campbell - Basel 2015
+
+
+structures = getAllenStructureList; %read structure data as a table
+
+data_sets = url2table('http://api.brain-map.org/api/v2/data/query.csv?criteria=model::SectionDataSet,rma::criteria,[id$in100141219,112423392,127084296,127866392,139426984,146858006,112424813],specimen%28injections%29,rma::options[tabular$eq%27distinct%20data_sets.id%20as%20section_data_set_id,injections.primary_injection_structure_id%27]');
+
+%Here we use arrayfun instead of the R sapply function
+data_sets.graph_order = arrayfun(@(x) structures.graph_order(structures.id == x), data_sets.primary_injection_structure_id);
+data_sets.acronym 	  = arrayfun(@(x) structures.acronym(structures.id == x), data_sets.primary_injection_structure_id);
+
+data_sets = sortrows(data_sets,'graph_order');
+
+
+unionizes = url2table('http://api.brain-map.org/api/v2/data/query.csv?criteria=model::ProjectionStructureUnionize,rma::criteria,section_data_set[id$in100141219,112423392,127084296,127866392,139426984,146858006,112424813],structure[acronym$in''VPL'',''VPM'',''PO'',''VAL'',''PF'',''VM'',''CM'',''RH'',''MD'',''PVT'',''RE'',''AM'',''AV'',''AD'',''LD'',''LP'',''LGv'',''LGd'',''MG''],rma::include,structure,rma::options[num_rows$eqall]');
+
+
+
+%This is much more long-winded than the R way: 
+%m = xtabs(projection_volume ~ section_data_set_id + structure_id, unionizes)
+setID = unique(unionizes.section_data_set_id);
+strID = unique(unionizes.structure_id);
+for ii=1:length(setID)
+	for jj=1:length(strID)
+		f=find(unionizes.section_data_set_id == setID(ii) & unionizes.structure_id == strID(jj));
+		m(ii,jj) = sum(unionizes.projection_volume(f));
+	end
+end
+
+
+%We now get the row and column names rather than use the ID numbers
+row_acronyms = arrayfun(@(x) data_sets.acronym(data_sets.section_data_set_id == x), setID);
+col_acronyms = arrayfun(@(x) structures.acronym(structures.id == x), strID);
+
+
+
+%Sort the rows and columns by sorted graph_order
+[~,row_order] = sort(arrayfun(@(x) data_sets.graph_order(data_sets.section_data_set_id == x), setID));
+[~,col_order] = sort(arrayfun(@(x) structures.graph_order(structures.id == x), strID));
+
+om = m(row_order,col_order);
+row_acronyms = row_acronyms(row_order);
+col_acronyms = col_acronyms(col_order);
+
+
+%Make the plot
+clf
+imagesc(om)
+set(gca,'YTick',1:size(om,1), 'YTickLabel',row_acronyms, 'XTick',1:size(om,2), 'XTickLabel',col_acronyms)
+colormap hot
+axis equal tight
+
+xlabel('target structure')
+ylabel('primary injection structure')
+title('Cortico-thalamic projection')
+
+
+
+
+%----------------------------------------------
+function thisTable=url2table(url)
+	%Read a URL into a table
+	thalamusTMP=fullfile(tempdir,'thalamus.csv');
+	urlwrite(url,thalamusTMP);
+    thisTable=readtable(thalamusTMP);
+    delete(thalamusTMP)

ARA/AllenBrainAPI-master/findAllenExperiments.m

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+function varargout = findAllenExperiments(varargin)
+% find all Allen experiments defined parameters
+%
+% function [IDs,json]=findAllenExperiments('param1','val1','param2','val2',...)
+%
+% 
+% Inputs
+% 'injection' - search for experiments with injections in this location. not searched for by default.
+%               this is case senstive. So 'VISp' searches for V1 but 'visp' produces an error.
+% 'line' - search for experiments on this transgenic line. not searched for by default. use '0' for wild-type, 
+% 'primary' - true/false. true by default, search for injections where 'injection' was the primary
+%             injection structure. if false it it will search for cases where 'injection' was not the primary
+%             structure.
+%
+%
+% Outputs
+% IDs - a vector of numbers corresponding to experiment IDs
+% json - cell array of structures containing all data pulled out of the JSON returned by the Allen API.
+%
+%
+% Examples
+% a) Return all experiments on wild type animals:
+% findAllenExperiments('line','0'); 
+%
+% b) Return all experiments with injections in V1
+% findAllenExperiments('injection','VISp'); 
+% or:
+% findAllenExperiments('injection','385'); 
+%
+% c) Return all experiments with injections in cortex
+% findAllenExperiments('injection','Isocortex'); 
+% 
+% Rob Campbell - Basel 2015
+%
+% requires JSONlab from the FEX
+%
+% See Also:
+% getInjectionIDfromExperiment
+
+
+if ~exist('loadjson')
+   disp('Please install JSONlab from the FEX') 
+   return
+end
+
+%Handle input arguments
+params = inputParser;
+params.CaseSensitive = false;
+params.addParamValue('injection','',@ischar)
+params.addParamValue('line','',@ischar)
+params.addParamValue('primary',true,@islogical)
+
+params.parse(varargin{:});
+
+
+%Build the URL 
+%this is the base URL
+url = 'http://api.brain-map.org/api/v2/data/query.json?criteria=service::mouse_connectivity_injection_structure';
+
+%now we extend it according to what is being searched
+if ~isempty(params.Results.injection)
+    url = [url,'[injection_structures$eq',params.Results.injection,']'];
+end
+
+if ~isempty(params.Results.line)
+    url = [url,'[transgenic_lines$eq',params.Results.line,']'];
+end
+
+if params.Results.primary
+    primary='true';
+else
+    primary='false';
+end
+url = [url,'[primary_structure_only$eq',primary,']'];
+
+
+
+%Get data from Allen
+page=urlread(url);
+result=loadjson(page);
+if ~result.success
+    fprintf('Query failed!\n%s\nAt URL: %s\n\n',result.msg,url);
+end
+
+
+%Return data
+IDs = ones(1,length(result.msg));
+for ii=1:length(IDs)
+    IDs(ii) = result.msg{ii}.id;
+end
+fprintf('Found %d experiments\n',length(IDs))
+
+
+
+if nargout>0
+    varargout{1}=IDs;
+end
+if nargout>1
+    varargout{2}=result.msg;
+end
+
+