title: IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 bins into which the IPL will be divided. Options to analyze tissues such as cortex were also added. Statistical analysis of the output then allows a quantitative value to be assigned to differences in laminar patterning observed in different models, genotypes or across developmental time.
  
  
  CONCLUSIONS
  IPLaminator is an easy to use software application that will greatly speed and standardize quantification of neuron organization.
authors.affiliation: Department of Biological Sciences, University of Idaho, 145 Life Science South, Moscow, ID, 83844, USA.
authors.forename: Shuai
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Computer Sciences, Lewis-Clark State College, Lewiston, ID, 83501, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Woodfin
authors.affiliation: Department of Computer Sciences, Lewis-Clark State College, Lewiston, ID, 83501, USA.
authors.forename: Seth S
authors.initials: SS
authors.lastname: Long
authors.affiliation: Department of Biological Sciences, University of Idaho, 145 Life Science South, Moscow, ID, 83844, USA. fuerst@uidaho.edu.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Fuerst
mesh_terms: D025042:Amacrine Cells / Q000166:cytology*; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D009415:Nerve Net; D016501:Neurites; D012165:Retinal Ganglion Cells / Q000166:cytology*; D012984:Software; D013569:Synapses