Neuron soma size and density measurements in male and female adult rat nucleus accumbens shell, nucleus accumbens core, and caudate-putamen disaggregated by sex and estrous cycle phase
Data files
Jul 24, 2025 version files 58.46 GB
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Cell_Data.xlsx
243.66 KB
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Data.7z
58.46 GB
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README.md
5.85 KB
Abstract
This dataset contains neuron soma size and density measurements from adult male and female rat striatal regions, including the nucleus accumbens shell, nucleus accumbens core, and caudate-putamen. The estrous cycle phase exhibited by the female rat was assessed, including the diestrus, proestrus, and estrus phases. Soma size and density properties across animals are presented in an analyzed format in a spreadsheet, as well as the individual calculations for each animal. Micrographs of Nissl-stained cells from each animal are also included in BMP format. These data provide the first measurements of striatal neuron soma size and density from adult gonad-intact animals and were key for revealing that the soma size of male neurons were bigger than female neurons in the nucleus accumbens shell.
Dataset DOI: 10.5061/dryad.zkh1893nk
Description of the data and file structure
ReadMe Document and data spreadsheets revised 6/24/25 by Nathan Dale and John Meitzen.
The Excel spreadsheet features neuron data of adult male and female wistar rats. Females were collected in different estrous cycle phases: diestrus, proestrus, and estrus cycle phases. Data collected was from the nucleus accumbens shell, nucleus accumbens core, and caudate-putamen, measuring soma size and density.
Files and variables
There are two types of files within this data set. The Microsoft Excel spreadsheet, named “cell_data”, contains individual quantified measurements of neuron soma size and density in each animal and region. The second file type within this data set is labeled “Data.7z” and contains .bmp files. BMP files are the micrographs taken of cells through a z-stack and can be opened using Fiji/ImageJ (https://imagej.net/software/fiji/downloads) or other photo/image software.
File Overview:
Cell_Data.xlsx
Cell_Data.xlsx is a Microsoft Excel spreadsheet containing the quantified data associated with this project. Besides Microsoft Excel, this file can be opened with Google Docs and Apache OpenOffice software. The spreadsheet contains 33 tabs. The “Master” tab contains summary data. Data are sorted into rows corresponding to each experimental animal and contain the Animal ID, Animal number for pictures and slides, Age of the animal (days), Sex of the animal (m=male, f=female), Estrous Cycle Phase, whether hemisphere was verified (N = no, Y = yes), and then neuron soma density (neurons/mm^3 x 10^3) and neuron soma size (microns^2) measurements sorted by region (NAc = Nucleus Accumbens; CPU = caudate-putamen). Regional data is presented encompassing both hemispheres, and also as sorted into right (R) and left (L) hemisphere data.
The subsequent tabs are each dedicated to a specific animal. There are 32 tabs for each of the 32 animals used in this study. Each tab labeled as Animal # is the corresponding Animal and its quantified data. For example, the Animal 1 tab is for Animal 1 and is linked to the Master tab. Animal data contains measurements categorized by physical location on the slide from which the images were obtained. The physical location is categorized in the following manner: T for top refers to the top row of brain slices, and B for bottom refers to the bottom row of brain slices. The second letter represents the position of the slice in the top or bottom row, left as L, middle as M, and right as R. The third letter represents either the left or right halves of the brain slice, L for left and R for right. So there will be labels such as “BLL,” “BML,” etc. For example, BML would be the bottom row, middle slice, left side of the tissue. Not all slide positions contributed measurements for each animal, so data will not be present in those locations. Acc stands for Nucleus Accumbens Core. Acsh stands for Nucleus Accumbens Shell. Cpu stands for Caudate-Putamen. ”Length”, “Width” and “Thickness” describe the counting box dimensions. “Left” and “Right” refer to brain hemisphere. “Density” stands for neuron soma density (neurons/mm^3 x 10^3) and “Area” stands for neuron soma size (microns^2). “Cells” indicates the number of cells analyzed.
Data.7z
The parent folder named “Data.7z” contains the image files associated with this project (41,102 BMP files). The data folder is zipped using the 7-Zip program and can be extracted using that program or WinRAR, WinZip, or The Unarchiver. Within the “Data” folder are folders dedicated to each of the 32 animals used in this study, named “Animal 1,” “Animal 2,” etc.). Within each Animal folder are folders dedicated to pictures taken from a slide of brain tissue, for example, slide “1.1” in “Animal 1.” Within each slide folder are folders dedicated to the assessed brain region. For example, there is a caudate-putamen folder labeled CPu, a nucleus accumbens core folder labeled Acc, and a nucleus accumbens shell folder labeled Acsh. Within each brain region folder are folders dedicated to the hemisphere from which the images were obtained, labeled left and right, respectively. Within each hemisphere folder, there are folders dedicated to the physical location of the slide from which the image was obtained. The first letter, T for top, refers to the top row of brain slices, and B for bottom refers to the bottom row of brain slices. The second letter represents the position of the slice in the top or bottom row, left as L, middle as M, and right as R. The third letter represents either the left or right halves of the brain slice, L for left and R for right. So there will be labels such as “BLL,” “BML,” etc. For example, BML would be the bottom row, middle slice, left side of the tissue. Within the physical location folder, there is a root folder labeled S_001. Within the root folder, there is a final folder labeled F_001. Within the final folder are the corresponding series of BMP files. The BMP image files are labeled in numerical order as imaged from the bottom to the top of the tissue section (e.g., Z-001.bmp, Z-002.bmp, etc.). Some of the folders will not contain BMP files. This absence means that photos were not taken from brain slices in that physical slide position. Thus, the total file structure will encompass the animal number, slide number, brain region, left or right hemisphere, physical location on slide, root folder S_001, and final folder F_001.
This dataset was collected using micrographs of nissl-stained striatal brain region tissue of adult male and female rats. The following brain regions were assessed: nucleus accumbens shell, nucleus accumbens core, and caudate-putamen. Striatal regions were assessed between 2.28-0.84 bregma. Counting box localization followed a previous study (Meitzen et al., 2011). For the CPu, the counting boxes were situated in the dorsomedial and dorsolateral portions. For the NAc core, the analyzed region encompassed both the medial and lateral areas adjacent to the anterior commissure. For the NAc shell, the region analyzed was medial to the lateral ventricle (commonly referred to as medial NAc shell). The nissl-stained neuron somas were analyzed to generate neuron soma size and density. These properties were then compared by striatal region, sex and female estrous cycle phase. More details can be found in the companion article, Dale et al., 2025, which is published in Brain Structure and Function (https://doi.org/10.1007/s00429-025-02995-5).