IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination

BMC Bioinformatics
Shuai LiPeter G Fuerst

Abstract

Information in the brain is often segregated into spatially organized layers that reflect the function of the embedded circuits. This is perhaps best exemplified in the layering, or lamination, of the retinal inner plexiform layer (IPL). The neurites of the retinal ganglion, amacrine and bipolar cell subtypes that form synapses in the IPL are precisely organized in highly refined strata within the IPL. Studies focused on developmental organization and cell morphology often use this layered stratification to characterize cells and identify the function of genes in development of the retina. A current limitation to such analysis is the lack of standardized tools to quantitatively analyze this complex structure. Most previous work on neuron stratification in the IPL is qualitative and descriptive. In this study we report the development of an intuitive platform to rapidly and reproducibly assay IPL lamination. The novel ImageJ based software plugin we developed: IPLaminator, rapidly analyzes neurite stratification patterns in the retina and other neural tissues. A range of user options allows researchers to bin IPL stratification based on fixed points, such as the neurites of cholinergic amacrine cells, or to define a number of bi...Continue Reading

References

Jun 1, 1986·The Journal of Comparative Neurology·T Voigt
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Dec 23, 2003·The Journal of Comparative Neurology·Krishna K GhoshHeinz Wässle
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Jul 27, 2011·Visual Neuroscience·Kevin J Ford, Marla B Feller
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Mar 15, 2012·Visual Neuroscience·Richard H Masland
Jan 31, 2014·The Journal of Comparative Neurology·Gabriel Belem de AndradePeter G Fuerst
Aug 3, 2014·The Journal of Physiology·Toshiyuki Ishii, Makoto Kaneda
Aug 28, 2014·Nature Reviews. Neuroscience·Thomas EulerTom Baden
Apr 10, 2015·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Shuai LiPeter G Fuerst

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Citations

Sep 1, 2017·The Journal of Comparative Neurology·Deborah L BeaudoinJonathan B Demb

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Software Mentioned

Image J
FIJI
IPLaminatorProject
ImageJ ProfilePlot
Image
IPLaminator

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