The organization of serotonergic fibers in the Pacific angelshark brain: Neuroanatomical and supercomputing analyses
Data files
Jul 14, 2025 version files 1.96 GB
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PacificAngelshark_CoronalSectionSet_Nissl.zip
734.44 MB
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PacificAngelshark_CoronalSectionSet_UnstainedWet.zip
634.23 MB
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PacificAngelshark_SimulatedFiberDensities.zip
592.04 MB
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Reader_SimulatedFiberDensities.nb
13.29 KB
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README.md
4.83 KB
Aug 21, 2025 version files 2.17 GB
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ContourGenerator_OneSection.zip
3.07 MB
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PacificAngelshark_CoronalSections_Serotonin-IHC.zip
202.15 MB
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PacificAngelshark_CoronalSectionSet_Nissl.zip
734.44 MB
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PacificAngelshark_CoronalSectionSet_UnstainedWet.zip
634.23 MB
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PacificAngelshark_SimulatedFiberDensities.zip
592.04 MB
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Reader_SimulatedFiberDensities.nb
13.29 KB
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README.md
6.24 KB
Abstract
Serotonergic axons (fibers) are a universal feature of all vertebrate brains. They form meshworks, typically quantified with regional density measurements, and appear to support neuroplasticity. The self-organization of this system remains poorly understood, partly because of the strong stochasticity of individual fiber trajectories. In an extension to our previous analyses of the mouse brain, serotonergic fibers were investigated in the brain of the Pacific angelshark (Squatina californica), a representative of a unique (ray-like) lineage of the squalomorph sharks. First, the fundamental cytoarchitecture of the angelshark brain was examined, including the expression of ionized calcium-binding adapter molecule 1 (Iba1, AIF-1) and the mesencephalic trigeminal nucleus. Second, serotonergic fibers were visualized with immunohistochemistry, which showed that fibers in the forebrain have the tendency to move toward the dorsal pallium and also accumulate at higher densities at pial borders. Third, a population of serotonergic fibers was modeled inside a digital model of the angelshark brain by using a supercomputing simulation. The simulated fibers were defined as sample paths of reflected fractional Brownian motion (FBM), a continuous-time stochastic process. The regional densities generated by these simulated fibers reproduced key features of the biological serotonergic fiber densities in the telencephalon, a brain division with a considerable physical uniformity and no major “obstacles” (dense axon tracts). These results demonstrate that the paths of serotonergic fibers may be inherently stochastic, and that a large population of such paths can give rise to a consistent, non-uniform, and biologically-realistic fiber density distribution. Local densities may be induced by the constraints of the three-dimensional geometry of the brain, with no axon guidance cues. However, they can be further refined by anisotropies that constrain fiber movement (e.g., major axon tracts, active self-avoidance, chemical gradients). In the angelshark forebrain, such constraints may be reduced to an attractive effect of the dorsal pallium, suggesting that anatomically complex distributions of fiber densities can emerge from the interplay of a small set of stochastic and deterministic processes.
Authors:
Skirmantas Janusonis, Ralf Metzler, Thomas Vojta
FILE: PacificAngelshark_CoronalSectionSet_Nissl.zip
This set of images is a series of coronal sections through a Pacific angelshark (Squatina californica) adult female brain. The specimen was collected in Santa Barbara County (California, USA) in September 2017.
The brain was embedded in gelatin (in two blocks) and sectioned at 40 micrometers thickness on a freezing microtome. The sections have been stained with a Nissl dye (thionine).
The sections are in the sequential rostro-caudal order, separated by 160 micrometers. The first section ("PacificAngelshark_Sp24_Thionine_1s1") contains a scale bar that applies to all sections with no magnification in the name. These images have been imaged in bright field with a 1X objective. Some images have two partially overlapping parts ("p1" and "p2").
Some details are shown at higher magnifications. These images have been captured in bright field and contain a scale bar (their names also include the magnification; e.g., "_5X").
Each physical slide had 6 mounted sections. The file name "PacificAngelshark_Sp24_Thionine_AsB" refers to the shark specimen number ("Sp24"), the slide number (A), and the section number (B) on this slide. Some sections in the middle of the set are incomplete (e.g., "14s1") because they were at the beginning of the second block.
The imaging system: Zeiss AxioImager Z1, with the following objectives: 1X (Plan-Neofluar, NA = 0.025), 5X (EC Plan-Neofluar, NA = 0.16), 10X (Plan-Apochromat, NA = 0.45), and 20X (Plan-Apochromat, NA = 0.80).
All sections have been processed and imaged by Dr. Skirmantas Janusonis (University of California, Santa Barbara).
FILE: PacificAngelshark_CoronalSectionSet_UnstainedWet.zip
This set of images is a series of coronal sections through a Pacific angelshark (Squatina californica) adult female brain. The specimen was collected in Santa Barbara County (California, USA) in September 2017.
The brain was embedded in gelatin (in two blocks) and sectioned at 40 micrometer thickness on a freezing microtome. The sections have been imaged on glass slides, unstained and uncoverslipped, after a quick dip in water.
The sections are in the sequential rostro-caudal order, separated by 160 micrometers. The first section ("PacificAngelshark_Sp24_Thionine_1s1") contains a scale bar that applies to all sections with no magnification in the name. These images have been imaged in bright field with a 1X objective. Some images have two partially overlapping parts ("p1" and "p2").
Each physical slide had 6 mounted sections. The file name "PacificAngelshark_Sp24_Thionine_AsB" refers to the shark specimen number ("Sp24"), the slide number (A), and the section number (B) on this slide. Some sections in the middle of the set are incomplete (e.g., "14s1") because they were at the beginning of the second block.
The imaging system: Zeiss AxioImager Z1, with a 1X objective (Plan-Neofluar, NA = 0.025).
All sections have been processed and imaged by Dr. Skirmantas Janusonis (University of California, Santa Barbara).
FILE: PacificAngelshark_SimulatedFiberDensities.zip
This dataset contains the simulated densities of 4800 serotonergic fibers modeled as fractional Brownian motion paths with Hurst index H = 0.8. Each path consists of 2^25 (approximately 33.6 million) steps. In the simulations, distances were measured in "pixel units" whose size corresponds to the size of the pixels in the images used to create the 3D-brain model. One pixel unit corresponds to 12.5 micrometers in the physical angelshark brain.
The fiber densities were recorded using a cubic grid with cells of linear size of 25.0 micrometers (i.e., 2 pixel-units). The densities are stored in the files 011.dat through 999.dat. Each file contains the densities at one rostrocaudal level (one coronal section). The filename indicates the rostrocaudal position in pixel units.
Each data file is organized in columns. The first three columns (igx, igy, igz) contain the labels (counters) of the grid cells in the three dimensions. The next three columns (x, y, x) contain the position of the center of each cell in pixel units. The seventh column (distrib) contains the fiber density, and the eighth column (log(distrib)) contains the natural log of distrib (or -100 if the density is zero). The densities are normalized as probability densities (i.e., the integral of the density over the entire shape is normalized to unity).
FILE: Reader_SimulatedFiberDensities.nb
This script (written in Wolfram Mathematica 14) reads simulated fiber densities (in the *.dat format) and outputs them as TIFF images.
FILE: ContourGenerator_OneSection.zip
This set contains the scripts (written in Wolfram Mathematica 14) used to generate brain contours for the supercomputing simulations. It is a two-step process, with a validation step (Steps 1-3). One brain section (#22) is shown as an example (PacificAngelshark_22.tif, with manually outlined contours in the other TIFF files). The set includes the executed Mathematica notebooks saved as PDF files and Excel (xlsx) files generated in the process (these files can be regenerated by running the scrips (nb), but they can also be opened without Mathematica).
FILE: PacificAngelshark_CoronalSections_Serotonin-IHC.zip
High-resolution (tiled) images of serotonergic fibers at eight coronal brain levels of an adult female Pacific angelshark (Squatina californica). The sections have been immunostained for serotonin (5-HT; ImmunoStar #20079) with the Cy3 fluorophore and imaged in color with a 5X objective (EC Plan-Neofluar, NA = 0.16) on a Zeiss AxioImager Z1 system. For details, see Janusonis et al. (2025) (https://doi.org/10.3389/fnins.2025.1602116). The sections have been processed and imaged by Dr. Skirmantas Janusonis (University of California, Santa Barbara).
Change Log
21 Aug 2025: two files were added: ContourGenerator_OneSection.zip and PacificAngelshark_CoronalSections_Serotonin-IHC.zip