Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Computational neuroanatomy: mapping cell-type densities in the mouse
  brain, simulations from the Allen Brain Atlas   The Allen Brain Atlas (ABA) of the adult mouse consists of digitized
expression profiles of thousands of genes in the mouse brain, co-registered to
a common three-dimensional template (the Allen Reference Atlas). This
brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy.
Its voxelized version (with cubic voxels of side 200 microns) can be analyzed
on a desktop computer using MATLAB. On the other hand, brain cells exhibit a
great phenotypic diversity (in terms of size, shape and electrophysiological
activity), which has inspired the names of some well-studied cell types, such
as granule cells and medium spiny neurons. However, no exhaustive taxonomy of
brain cells is available. A genetic classification of brain cells is under way,
and some cell types have been characterized by their transcriptome profiles.
However, given a cell type characterized by its transcriptome, it is not clear
where else in the brain similar cells can be found. The ABA can been used to
solve this region-specificity problem in a data-driven way: rewriting the
brain-wide expression profiles of all genes in the atlas as a sum of
cell-type-specific transcriptome profiles is equivalent to solving a quadratic
optimization problem at each voxel in the brain. However, the estimated
brain-wide densities of 64 cell types published recently were based on one
series of co-registered coronal in situ hybridization (ISH) images per gene,
whereas the online ABA contains several image series per gene, including
sagittal ones. In the presented work, we simulate the variability of cell-type
densities in a Monte Carlo way by repeatedly drawing a random image series for
each gene and solving optimization problems. This yields error bars on the
region-specificity of cell types.

15
The categories of this paper are: nucl-ex
13
The categories of this paper are: quant-ph
23
The categories of this paper are: solv-int
30
The categories of this paper are: q-alg
4
The categories of this paper are: cond-mat
11
The categories of this paper are: hep-lat
0
The categories of this paper are: hep-ph
27
The categories of this paper are: comp-gas
9
The categories of this paper are: nlin
5
The categories of this paper are: gr-qc
20
The categories of this paper are: acc-phys
33
The categories of this paper are: plasm-ph
37
The categories of this paper are: supr-con
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The categories of this paper are: hep-th
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The categories of this paper are: dg-ga
32
The categories of this paper are: atom-ph