Blog Archives
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
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
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
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
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
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
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
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
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 These files are shared under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/).
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