How to Prepare Neuroanatomical Image Data

Nathan O'Connor1, Susan Tappan2, Jacob Glaser2

1 MBF Bioscience, Williston, Vermont, 2 MBF Laboratories, Williston, Vermont
Publication Name:  Current Protocols in Neuroscience
Unit Number:  Unit 1.21
DOI:  10.1002/0471142301.ns0121s69
Online Posting Date:  October, 2014
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Abstract

As image data from a single neuroanatomical study can easily exceed tens of gigabytes, managing, analyzing, and presenting it is not trivial. Careful planning along multiple axes is required and includes the following: (1) Organizational methods developed for images should allow for easy and efficient access, selection, and potential reorganization of images. (2) Experimental information and other metadata should be readily available and accompany image data. (3) Even if a study's entire body of image data is made available, highlighting key results and preparing figures requires selecting image regions and resolutions, creating annotations, and adhering to publishing and community guidelines for image adjustments. Further, it may be necessary to assess Internet accessibility and infrastructure issues and to consider image formats appropriate for Web publishing. Finally, a strategy for robust, long‐term, and efficient storage of image data should be developed. This unit provides a guide for preparing neuroanatomical image data. Curr. Protoc. Neurosci. 69:1.21.1‐1.21.14. © 2014 by John Wiley & Sons, Inc.

Keywords: whole‐slide imaging; image management; virtual slides; big data; virtual tissue

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Naming and Organization of Images and Metadata
  • Basic Protocol 2: Preparing and Annotating Images for Presentations and Figures
  • Basic Protocol 3: Assessing Internet Environment and Optimizing Images
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Gaillard, F., Karten, H.J., and Sauvé, Y. 2013. Retinorecipient areas in the diurnal murine rodent Arvicanthis niloticus: A disproportionally large superior colliculus. J. Comp. Neurol. 521:1699‐1726.
  Gerfen, C.R., Paletzki, R., and Heintz, N. 2013. GENSAT BAC Cre‐recombinase driver lines to study the functional organization of cerebral cortical and basal ganglia circuits. Neuron 80:1368‐1383.
  Kalinski, T., Zwönitzer, R., Grabellus, F., Sheu, S.‐Y., Sel, S., Hofmann, H., and Roessner, A. 2011. Lossless compression of JPEG2000 whole slide images is not required for diagnostic virtual microscopy. Am. J. Clin. Pathol. 136:889‐895.
  Karten, H.J., Glaser, J.R., and Hof, P.R. 2013. An important landmark in scientific publishing. J. Comp. Neurol. 521:1697‐1698.
  Mikula, S., Trotts, I., Stone, J.M., and Jones, E.G. 2007. Internet‐enabled high‐resolution brain mapping and virtual microscopy. NeuroImage 35:9‐15.
  Rossner, M. and Yamada, K.M. 2004. What's in a picture? The temptation of image manipulation. J. Cell Biol. 166:11‐15.
  Tuominen, V.J. and Isola, J. 2009. The application of JPEG2000 in virtual microscopy. J. Digital Imag. 22:250‐258.
  Weinstein, R.S., Graham, A.R., Richter, L.C., Barker, G.P., Krupinski, E.A., Lopez, A.M., Erps, K.A., Bhattacharyya, A.K., Yagi, Y., and Gilbertson, J.R. 2009. Overview of telepathology, virtual microscopy, and whole slide imaging: Prospects for the future. Human Pathol. 40:1057‐1069.
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