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Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex

Version 1.0

Majka, Piotr, 2025, "Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex", https://doi.org/10.18150/NT1X3Z, RepOD, V1

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Description

The dataset contains three-dimensional, whole-brain density maps of neurons expressing the calcium-binding protein Calbindin (CB+) of three individuals (F, 3 years, 5 months, 309.5 g; F, 3 years, 7 months, 20 days, 441 g; M, 3 years 7 months, 21 days, 343 g) of the Common Marmoset (Callithrix jacchus) monkey.

For each hemisphere, every fifth section covering the entire brain was processed with diaminobenzidine (DAB) immunohistochemistry using a monoclonal antibody (AB_10000347). Stained sections were scanned using an Aperio Scanscope AT Turbo (Leica Biosystems) at ×20 magnification. Subsequently, the density maps were computed using a combination of automated cell identification, three-dimensional reconstruction, and cytoarchitecture-aware registration.

The results are provided as Neuroimaging Informatics Technology Initiative (NIfTI) datasets, spreadsheets, and Python scripts and datasets to reproduce the deep learning model for automated cell identification.


(2024-09-23)
Subject
Medicine, Health and Life Sciences
Keyword

quantitative cytoarchitecture, calcium-binding protein, cortical areas, Callithrix jacchus, microscopy images, deep learning

Related Publication

Atapour N, Rosa MGP, Bai S, Bednarek S, Kulesza A, et al. (2024) Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex. PLOS Computational Biology 20(9): e1012428. https://doi.org/10.1371/journal.pcbi.1012428 https://doi.org/10.1371/journal.pcbi.1012428 doi: 10.1371/journal.pcbi.1012428

CC BY - Creative Commons Attribution 4.0 CC BY - Creative Commons Attribution 4.0

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1 to 7 of 7 Files
Atapour_et_al_2024_CB_density_maps.zip
ZIP Archive - 123.6 MB - Mar 18, 2025 - 1 Download
MD5: 8e1c84b44828faee5b7d008122181a52
License: CC BY - Creative Commons Attribution 4.0
For each of the three cases (CJ1741, CJ200L, and CJ205) the following datasets are available: {case_id}_CB_density_map.nii.gz Three-dimensional image of the density map of CB+ neurons (in mm-3). {case_id}_3d_reconstruction.nii.gz Three-dimensional image of the calbindin sections. The image is compatible with the density map. {case_id}_segmentation_into_areas.nii.gz Segmentation of the cortex into areas areas. To be used together with the atlas_labels.txt label description file. {case_id}_segmentation_into_layers.nii.gz Segmentation of the cortex into supragranular (I-III), granular (IV), and infragranular (VI) cell layers. {case_id}_mask.nii.gz Mask used to calculate the values reported in Supplemental Table 1. The mask takes into account the artifacts and other parts of the tissue (i.e. Layer 1) that were decided to be excluded from the analyses. atlas_labels.txt A file containing label descriptions for the segmentation into cortical areas.
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Supporting_Table_S1.ods
Unknown - 82.0 KB - Mar 18, 2025 - 1 Download
MD5: 3ce68912b91ae6cf65c373ff12612dd7
License: CC BY - Creative Commons Attribution 4.0
Source dataset for reproducing analyses presented in Figure 3-7 of the related publication.
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Supporting_Table_S2.ods
Unknown - 53.0 KB - Mar 18, 2025 - 0 Downloads
MD5: 9e41e0b9fc7b3bd2ef6429ef7b1faee5
License: CC BY - Creative Commons Attribution 4.0
Source dataset for analyses of the variance in densities.
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Supporting_Table_S3.ods
Unknown - 26.9 KB - Mar 18, 2025 - 0 Downloads
MD5: 4c4002a8f95019c35dc0bdfffbcf2bad
License: CC BY - Creative Commons Attribution 4.0
Source dataset for valuation of the registration accuracy.
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Supporting_File_S1.pdf
Adobe PDF - 1011.1 KB - Mar 18, 2025 - 0 Downloads
MD5: 87a2581de6b8f224301b0f1de190228b
License: CC BY - Creative Commons Attribution 4.0
Supporting File S1: Reference card with the full names, abbreviations, color-codes and flatmap locations of the individual cortical areas, groups of areas, and the cytoarchitectural categories of lamination.
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Atapour_et_al_2024_CB_density_maps_training_code.zip
ZIP Archive - 589.3 MB - Mar 18, 2025 - 0 Downloads
MD5: 32be707b076f67223228bab5a191767a
License: CC BY - Creative Commons Attribution 4.0
Python scripts for training the Unet CNN and the input NumPy datasets.
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Atapour_et_al_2024_CB_images_and_annotations.zip
ZIP Archive - 1.9 GB - Mar 18, 2025 - 0 Downloads
MD5: 478f42c19de2e6b39eb0b039aff95deb
License: CC BY - Creative Commons Attribution 4.0
The dataset used for training and validation of the Unet CNN: The training dataset contains 196 image strips (3,429 counting boxes) used to train the Unet CNN model. The validation dataset contains 54 image strips (603 counting boxes) used to evaluate the model’s performance. The benchmark dataset contains 81 image strips (939 counting boxes) used to compare the Unet CNN against multiple human raters. Each dataset contains a series of TIFF files containing the image strips extracted from the high-resolution microscopic (0.4974 µm per pixel) images. They are accompanied by corresponding SVG files containing annotations (definitions of counting boxes and individual cells).
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