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Neurite_FISH_Quant–Python code for quantification of FISH puncta in neurites

By Ben Hobson, BA, Linghao Kong, Maria F. Angelo, Ori J. Lieberman, Eugene Mosharov, PhD, Etienne Herzog, David Sulzer, PhD and Peter Sims, PhD
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Output Details

Description

This repository contains Jupyter Notebooks with Python 3 code for quantification of FISH puncta within neuronal dendrites or axons. However, prior identification of FISH puncta in the images (and optional neurite segmentation) is required. We use ImageJ plugins for this purpose, as specified below. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.

Identifier (DOI)
10.5281/zenodo.5570748
Team
Team Sulzer
Program
Collaborative Research Network
Theme
Neuro-Immune Interactions

Meet the Authors

  • Ben Hobson, BA

    Key Personnel: Team Sulzer, 

    Columbia University

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    Linghao Kong

    External Collaborator

  • User avatar fallback logo

    Maria F. Angelo

    External Collaborator

  • User avatar fallback logo

    Ori J. Lieberman

    External Collaborator

  • Eugene Mosharov, PhD

    Key Personnel: Team Sulzer, 

    Columbia University

  • User avatar fallback logo

    Etienne Herzog

    External Collaborator

  • David Sulzer, PhD

    Lead PI (Core Leadership): Team Sulzer, 

    Columbia University

  • Peter Sims, PhD

    Key Personnel: Team Sulzer, 

    Columbia University

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