Skip to main content
SpringerLink
Log in

Point Analysis in Java Applied to Histological Images of the Perforant Pathway: A User’s Account

  • Commentary
  • Published:
Neuroinformatics Aims and scope Submit manuscript

Abstract

The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (×2 objective) comprised the entire perforant pathway, while the high magnification set (×100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  • Abramoff, M. D., Magelhaes, P. J., & Ram, S. J. (2004). Image Processing with ImageJ. Biophotonics International, 7, 36–42.

    Google Scholar 

  • Ascoli, G. A., & Scorcioni, R. (2006). Neuron and network modeling. In L. Zaborszky, F. G. Wouterlood, & J. Lanciego (Eds.) Tract tracing methods ((pp. 604–630)3rd ed.). New York: Springer.

    Google Scholar 

  • Condron, B. (2008). A freeware Java tool for the spatial point analysis of neuronal structures. Neuroinformatics, (in press).

  • Reiner, A., Veenman, C. L., Medina, L., Jiao, Y., Del Mar, N., & Honig, M. G. (2000). Pathway tracing using biotinylated dextran amines. Journal of Neuroscience Methods, 103, 23–37.

    Article  PubMed  CAS  Google Scholar 

  • Van Groen, T. (2001). Entorhinal cortex of the mouse: cytoarchitectonical organization. Hippocampus, 11, 397–407.

    Article  PubMed  Google Scholar 

  • Van Groen, T., Miettinen, P., & Kadish, I. (2003). The entorhinal cortex of the mouse: organization of the projection to the hippocampal formation. Hippocampus, 13, 8133–149.

    Article  Google Scholar 

  • Witter, M. P. (2007). The perforant path: projections from the entorhinal cortex to the dentate gyrus. Progress in Brain Research, 163, 43–61.

    Article  PubMed  Google Scholar 

  • Wouterlood, F. G., & Jorritsma-Byham, B. (1993). The anterograde neuroanatomical tracer biotinylated dextran-amine: comparison with the tracer Phaseolus vulgaris-leucoagglutinin in preparations for electron microscopy. Journal of Neuroscience Methods, 48, 75–87.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by NIH R01 grants NS39600 and NS24288.

Author information

Authors and Affiliations

  1. Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, 22030, USA

    Ruggero Scorcioni, Susan N. Wright & Giorgio A. Ascoli

  2. Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, 15260, USA

    J. Patrick Card & Germán Barrionuevo

Authors
  1. Ruggero Scorcioni
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Susan N. Wright
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Patrick Card
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Giorgio A. Ascoli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Germán Barrionuevo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ruggero Scorcioni.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Scorcioni, R., Wright, S.N., Patrick Card, J. et al. Point Analysis in Java Applied to Histological Images of the Perforant Pathway: A User’s Account. Neuroinform 6, 63–67 (2008). https://doi.org/10.1007/s12021-008-9011-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12021-008-9011-4

Keywords

Search

Navigation