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Verpeut et al. Y-maze c-Fos brain samples

This page contains links to interactive visualizations of brain-wide c-Fos expression and cerebellar injection site localization from mouse subjects studied in the manuscript “Cerebellar contributions to a brainwide network for flexible behavior” by Jessica L. Verpeut et al. (pdf: https://www.biorxiv.org/content/10.1101/2021.12.07.471685v1). … Continue reading

06. January 2022 by ahoag
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Python package for brain atlas manipulation now available on PyPI

We recently released a Python package called brain-atlas-toolkit to the Python Package Index (PyPI.org). This means that you can now obtain this package via: pip install brain-atlas-toolkit This package provides tools for navigating hierarchical brain atlases, such as the Allen … Continue reading

04. October 2021 by ahoag
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Pisano et al. viral tracing injection sites

This page contains links to interactive visualizations of the volumetric cerebellar injection sites described in the manuscript: “Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain” by Thomas J Pisano et al.: https://www.sciencedirect.com/science/article/pii/S2211124721011700 Injection sites were identified in … Continue reading

18. May 2021 by ahoag
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The Python interface to Neuroglancer

The Python interface to Neuroglancer provides several advantages over using fixed links to your data, such as the visualization links generated at the braincogs00.pni.princeton.edu site. The main advantage is that it gives you programmatic control over your Neuroglancer session. A … Continue reading

19. March 2021 by ahoag
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Displaying atlas region boundaries in Neuroglancer

We recently added the three dimensional atlas developed by Chon et al. 2019 (PI Yongsoo Kim; Penn State; https://www.nature.com/articles/s41467-019-13057-w) as an option to which we can register your mouse brain light sheet images using our automatic brain registration pipeline, BrainPipe. … Continue reading

04. December 2020 by ahoag
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Using the Neuroglancer search/filter tool

There are several ways to select which segments to display in Neuroglancer. One we have already covered in the “Getting Started with Neuroglancer” post is double clicking individual segments to select them. This works well if you already know exactly … Continue reading

13. November 2020 by ahoag
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New Neuroglancer feature: import annotations from CSV files

Annotations are a useful feature of Neuroglancer. In previous posts, we’ve gone over how to add annotations to mark regions of interest in our lightsheet volumes. In the Brain Registration and Histology Core Facility at PNI, we also frequently use … Continue reading

15. October 2020 by ahoag
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Visualizing different levels of the brain atlas structure hierarchy graph in Neuroglancer

Brain atlases, such as the Allen Mouse Brain Atlas (AMBA) and Princeton Mouse Brain Atlas (PMA) are invaluable tools. They allow data from different experiments to be compared and analyzed in the same framework. With Neuroglancer and other visualization tools, … Continue reading

24. September 2020 by ahoag
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Princeton Mouse Brain Atlas links

Interactive 2D/3D Neuroglancer volume: https://brainmaps.princeton.edu/pma_neuroglancer Atlas tissue volume: https://brainmaps.princeton.edu/pma_tissue Atlas annotation volume: https://brainmaps.princeton.edu/pma_annotations Atlas id to name mapping: https://brainmaps.princeton.edu/pma_id_table Atlas structure ontology list: https://nbviewer.jupyter.org/github/PrincetonUniversity/lightsheet_helper_scripts/blob/master/projects/combine_cfos_batches/data/PMA_regions.html

02. September 2020 by ahoag
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Probe Detection Example with Neuroglancer

One of the common use cases of the light sheet microscope at PNI is post-experiment validation of the anatomical location of a probe inserted into a rodent brain for neural recording. The following video illustrates via example how to use … Continue reading

06. August 2020 by ahoag
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