Downloads

“Flattened Cortical Maps of Cerebral Function in the Rat:  A Region-of-Interest Approach to Data Sampling, Analysis and Display”, Holschneider DP, Scremin OU, Chialvo DR, Kay BP, Maarek J-MI, Neuroscience Letters, in press, 2008

ABSTRACT:  We describe a method for the measurement, analysis and display of cerebral cortical data obtained from coronal brain sections of the adult rat.  In this method, regions-of-interest (ROI) are selected in the cortical mantle in a semiautomated fashion using a radial grid overlay, spaced in 15 degree intervals from the midline. ROI measurements of intensity are mapped on a flattened two-dimensional surface. Topographic maps of statistical significance at each ROI allow for the rapid viewing of group differences.  Cortical z-scores are displayed with the boundaries of brain regions defined according to a standard atlas of the rat brain.  This method and accompanying software implementation (Matlab, Labview) allow for compact data display in a variety of autoradiographic and histologic studies of the structure and function of the rat brain.

Overview:  This article is accompanied by the files listed below.

PDF version of the article:  ‘Article.pdf’

Extended protocol for use:  This file reproduces the text in the publication’s methods and adds additional explanatory detail, ‘Extended Protocol.doc’ (Microsoft Word)

Cortical ROI Selector, Version 1.0:  ‘CxROISelector v1 0.m’ selects regions of interest within the cortex of rat coronal brain slices.  The program has been tested with Matlab version 6.5.1, release 13 and Matlab 7.1.0.21, release 14 (The Mathworks).  Versions of Matlab can be need to be purchased by the user.

Interactive ROI Reporter, Version 1.0:  ‘Interactive ROI Reporter v1 0.exe’, display and analysis of the cortical data. ROI analysis and topographic mapping is performed on the ASCII data obtained from the cortical ROI selector using a custom software program written in LabVIEW (National Instruments, Version 8.2).  The user can download free of charge the LABVIEW runtime engine from the publisher’s website.

Sample data folder:
(1) For Cortical ROI selection program

  • Sample Images:
    SampleExpt%G18R02_S04A.tif
    SampleExpt%G18R02_S05A.tif
    SampleExpt%G18R02_S08A.tif
    SampleExpt%G18R02_S011C.tif
    SampleExpt%G18R02_S15b.tif

(2)For Interactive ROI Reporter

  • Data file generated by ROI selection program, ‘Data.txt’
  • a file describing for each animal the slice containing the coregistration landmark (AP -0.3 mm relative to bregma), ‘Landmark -0 3.txt’
  • a table identifying for each bregma level a number identifying the subset of the possible 10 ROIs to be analyzed in each hemisphere ‘ROIs to retain.txt’ (from Paxinos & Watson 2005 rat brain atlas)

Download files:  Files are provided free of charge.  Downloaded files are for noncommercial, public use.

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