PyNutil

a Python library for brain-wide quantification and spatial analysis of features in serial section images from the brain.

Getting Started

Installation, supported formats and key concepts.

Getting started

GUI

Use PyNutil via the graphical user interface.

GUI

Gallery

A gallery of examples using PyNutil.

Gallery

Overview

PyNutil is able to integrate outputs from various atlas registration software and image segmentation software in order to produce atlas based quantifications, 3D point clouds, and 3D heatmaps of brain derived data.

PyNutil aims to replicate and expand the Quantifier feature of the Nutil software (RRID: SCR_017183).

Warning

PyNutil is still under development and the API is subject to change.

The documentation below brings together installation notes, the basic workflow, practical examples, and the generated API reference.

Contents:

• Getting started
  • Installation
  • Choose your workflow
  • First successful run
  • Inputs PyNutil expects
  • Core workflows
  • Outputs
  • Interpolated 3D volumes
  • Worked examples
  • Troubleshooting
• GUI
  • Installation
  • What the GUI does
  • Required inputs
  • Atlas choices
  • Segmentation and intensity modes
  • Optional volume interpolation
  • Output folders
• Gallery
• API
  • Top-level functions
  • Result classes

Highlights

• Use BrainGlobe atlases or custom atlas volumes in .nrrd format.

• Read registration data from QuickNII, VisuAlign, DeepSlice, or BrainGlobe registration outputs.

• Quantify binary segmentations or intensity images against atlas regions.

• Export point clouds for MeshView and interpolated NIfTI volumes for siibra explorer or ITK-SNAP.

For more background on the QUINT workflow, see QUINT workflow documentation.

Index & Search

• Index

• Search Page