Tools to analyze the supplemental data from The Allen Institute's publication of their mouse connectome atlas in 2014: Nature (508)207--217. The suppl data reveal large scale connectivity between brain regions, allowing you to ask questions of the data without having to use the much more detailed (but larger/more difficult) raw data available from the Allen's website.
See saved data.docx for some analyese I ran to look at HPC connectivity. A fast example is below:
[Presm Postsm]=whosConnected('ENTm',Wipsi,Areas,AreasLookup,Pipsi,0.2); Presm
Presm =
'Entorhinal area, lateral part' [0.3317] [2.9865e-66]
'Medial septal nucleus' [0.4397] [7.6496e-24]
'Parasubiculum' [0.7726] [5.8431e-21]
'Nucleus of reunions' [0.2745] [1.0476e-14]
'Diagonal band nucleus' [0.2626] [6.0253e-09]
'Parataenial nucleus' [1.2141] [1.4927e-05]
'Subiculum, ventral part' [0.1288] [3.8951e-04]
[1x41 char] [0.1397] [4.1244e-04]
'Postsubiculum' [0.4902] [ 0.0014]
'Subiculum, dorsal part' [0.1480] [ 0.0021]
'Lateral visual area' [0.1680] [ 0.0049]
'Posterior amygdalar nucleus' [0.8548] [ 0.0294]
'Posterolateral visual area' [0.1525] [ 0.0350]
'Claustrum' [0.4798] [ 0.0377]
'Field CA1' [0.0727] [ 0.0389]
[1x34 char] [0.8072] [ 0.0473]
'Dentate gyrus' [0.0462] [ 0.0714]
'Field CA3' [0.0465] [ 0.0764]
'Basolateral amygdalar nucleus' [0.1215] [ 0.0781]
'Endopiriform nucleus, dorsal part' [0.2363] [ 0.1155]
'Piriform-amygdalar area' [0.2833] [ 0.1556]
'Medial mammillary nucleus' [0.2955] [ 0.1618]
This list shows brain regions that send inputs to the medial entorhinal cortex. The first column is the "weight" of the connection, the second column is a p-value indicating the probability of of a null hypothesis of accidentally observing this connectivity given there was not actually any anatomical basis for it.
Put this in a directory and cd to it in Matlab. You're done.
Jason G. Fleischer
You are free to use and distribute this code as you see fit. Please credit the original author.