DOI: 10.25349/d95w36
title: Data from: An experimental platform for stochastic analyses of single serotonergic fibers in the mouse brain

description: The self-organization of the serotonergic matrix, a massive axon meshwork
 in all vertebrate brains, is driven by the structural and dynamical
 properties of its constitutive elements. Each of these elements, a single
 serotonergic axon (fiber), has a unique trajectory and can be supported by
 a soma that executes one of the many available transcriptional programs.
 This “individuality” of serotonergic neurons necessitates the development
 of specialized methods for single-fiber analyses, both at the experimental
 and theoretical levels. We developed an integrated platform that
 facilitates experimental isolation of single serotonergic fibers in brain
 tissue, including regions with high fiber densities, and demonstrated the
 potential of their quantitative analyses based on stochastic modeling.
 Single fibers were visualized using two transgenic mouse models, one of
 which is the first implementation of the Brainbow toolbox in this system.
 The trajectories of serotonergic fibers were automatically traced in the
 three spatial dimensions with a novel algorithm, and their properties were
 captured with a single parameter associated with the directional von
 Mises-Fisher probability distribution. The system represents an end-to-end
 workflow that can be imported into various studies, including those
 investigating serotonergic dysfunction in brain disorders. It also
 supports new research directions inspired by single-fiber analyses in the
 serotonergic matrix, including supercomputing simulations and modeling in
 physics.
description: The z-stack named "zStack_EGFP.zip" is a zipped
 3D-image of the inferior colliculus in the brain of an adult mouse that
 expresses EGFP (enhanced green fluorescent protein) in serotonergic fibers
 (after Tph2-dependent Cre recombination). The image was acquired on a
 Leica SP8 resonant scanning confocal system with a 60xoil (NA 1.40)
 objective. Each image is 3144 x 3144 pixels, with the XY-scaling of 59
 nm/pixel and the Z-step (between consecutive images) of 299 nm. The images
 have been converted to grayscale and autocontrasted. The set includes a
 maximum-intensity projection (an RGB image). Three Wolfram Mathematica
 notebooks (executable code) are included
 ("SingleFiberAnalysis_Step1_EGFP-Trace1.nb",
 "SingleFiberAnalysis_Step2.nb",
 "SingleFiberAnalysis_Step3.nb") that trace and analyze one fiber
 in the image. The notebooks can be used in other
 datasets.<br> <br>The z-stack named
 "zStack_Brainbow.zip" is a zipped 3D-image of the basolateral
 amygdala in the brain of an adult mouse that expresses Brainbow
 fluorophores in serotonergic fibers (after Tph2-dependent Cre
 recombination). The image was acquired on a Leica SP8 resonant scanning
 confocal system with a 60xoil (NA 1.40) objective. Each image is 2552 x
 2552 pixels, with the XY-scaling of 72 nm/pixel and the Z-step (between
 consecutive images) 299 nm. The original (not autocontrasted) images in
 the three fluorophore channels (ch0, ch1, ch2) are named
 "Brainbow_M18_AF488_AF594_AF647_AmygdalaBLARegion" and the
 merged channels (converted to grayscale and autocontrasted) are named
 "BLA". The set includes a maximum-intensity projection (an RGB
 image). Three Wolfram Mathematica notebooks (executable code) are included
 ("SingleFiberAnalysis_Step1_Brainbow-Trace(1-3).nb") that trace
 three fibers in the image. The notebooks can be used in other
 datasets. The z-stack named
 "zStack_Brainbow-Subset.zip" is an XY-subset of
 "zStack_Brainbow." Specifically, the original z-stack has been
 subsetted in the XY-plane but retains all optical sections (in the
 Z-dimension). The pixel scaling is the same as in the original image. The
 set includes the merged channels (converted to grayscale and
 autocontrasted), which are named "Subset_BLA", and a
 maximum-intensity projection (an RGB image). Twenty Wolfram Mathematica
 notebooks (executable code) are included
 ("SingleFiberAnalysis_Step1_BrainbowSubset-Trace(1-20).nb") that
 trace twenty fibers in the image. The notebooks can be used in other
 datasets. The traced fibers can be analyzed as a set with
 "SingleFiberAnalysis_Step2_BrainbowSubset.nb" and
 "SingleFiberAnalysis_Step3_BrainbowSubset.nb".
  <br> <br>The Wolfram Mathematica notebooks
 "Simulator_SingleFiber.nb" and
 "Simulator_BrainbowFibers.nb" generate a single monochrome fiber
 and a set of Brainbow fibers, respectively.
description: An Experimental Platform for Stochastic Analyses of Single Serotonergic
 Fibers in the Mouse Brain Kasie C. Mays, Justin H. Haiman, Skirmantas
 Janusonis University of California, Santa Barbara The z-stack named
 "zStack\_EGFP.zip" is a zipped 3D-image of the inferior
 colliculus in the brain of an adult mouse that expresses EGFP (enhanced
 green fluorescent protein) in serotonergic fibers (after Tph2-dependent
 Cre recombination). The image was acquired on a Leica SP8 resonant
 scanning confocal system with a 60xoil (NA 1.40) objective. Each image is
 3144 x 3144 pixels, with the XY-scaling of 59 nm/pixel and the Z-step
 (between consecutive images) of 299 nm. The images have been converted to
 grayscale and autocontrasted. The set includes a maximum-intensity
 projection (an RGB image). Three Wolfram Mathematica notebooks (executable
 code) are included
 ("SingleFiberAnalysis\_Step1\_EGFP-Trace1.nb",
 "SingleFiberAnalysis\_Step2.nb",
 "SingleFiberAnalysis\_Step3.nb") that trace and analyze one
 fiber in the image. The notebooks can be used in other datasets. The
 z-stack named "zStack\_Brainbow.zip" is a zipped 3D-image of the
 basolateral amygdala in the brain of an adult mouse that expresses
 Brainbow fluorophores in serotonergic fibers (after Tph2-dependent Cre
 recombination). The image was acquired on a Leica SP8 resonant scanning
 confocal system with a 60xoil (NA 1.40) objective. Each image is 2552 x
 2552 pixels, with the XY-scaling of 72 nm/pixel and the Z-step (between
 consecutive images) 299 nm. The original (not autocontrasted) images in
 the three fluorophore channels (ch0, ch1, ch2) are named
 "Brainbow\_M18\_AF488\_AF594\_AF647\_AmygdalaBLARegion" and the
 merged channels (converted to grayscale and autocontrasted) are named
 "BLA". The set includes a maximum-intensity projection (an RGB
 image). Three Wolfram Mathematica notebooks (executable code; added in the
 first update) are included
 ("SingleFiberAnalysis\_Step1\_Brainbow-Trace(1-3).nb") that
 trace three fibers in the image. The notebooks can be used in other
 datasets. The z-stack named "zStack\_Brainbow-Subset.zip" (added
 in the second update) is an XY-subset of "zStack\_Brainbow."
 Specifically, the original z-stack has been subsetted in the XY-plane but
 retains all optical sections (in the Z-dimension). The pixel scaling is
 the same as in the original image. The set includes the merged channels
 (converted to grayscale and autocontrasted), which are named
 "Subset\_BLA", and a maximum-intensity projection (an RGB
 image). Twenty Wolfram Mathematica notebooks (executable code) are
 included
 ("SingleFiberAnalysis\_Step1\_BrainbowSubset-Trace(1-20).nb")
 that trace twenty fibers in the image. The notebooks can be used in other
 datasets. The traced fibers can be analyzed as a set with
 "SingleFiberAnalysis\_Step2\_BrainbowSubset.nb" and
 "SingleFiberAnalysis\_Step3\_BrainbowSubset.nb". The Wolfram
 Mathematica notebooks "Simulator\_SingleFiber.nb" and
 "Simulator\_BrainbowFibers.nb" generate a single monochrome
 fiber and a set of Brainbow fibers, respectively.