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Cut image volumes along arbitrary surfaces

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What is VolumeCut?

VolumeCut is a MATLABĀ® app that allows you to cut a volumetric image along arbitrary defined surfaces.

This software is developed for neuroscience research purposes, where it is able to segment regions of the nervous system along their physiological curvature.

VolumeCut is licensed under GNU General Public License v3. This strong copyleft license ensures you will always have the right to obtain, view and modify VolumeCut's source code to review its functionality and improve its features.

We strongly believe that software developed for data analysis in scientific research must be open source, to ensure the highest level of reproducibility of your science.

Runs on your favorite platform

Whether your workstation relies on Microsoft Windows, macOS or Linux, VolumeCut can run on your computer since it relies only on core Matlab functions.

Having a single code base for all platforms makes developing new features as well as fixing bugs a much faster and enjoyable journey.

Visually interact with your data

VolumeCut can display the interpolated surfaces in 3D in order to check quality before cutting the volume.

VolumeCut can preview the cut volumes as well as the source volume using the internal 3D renderer.

You can visually zoom, rotate and pan through the volume using your mouse.

Visualize and modify 3D masks

Visualize 3D binary masks generated by VolumeCut as well as other 3D image analysis apps like ImageJ. Scroll your mouse wheel to navigate the mask volume.

VolumeCut allows you to modify in 3D the binary mask and perform logical operations between two masks. You can for example: invert colors, find edges, unite, intersect, subctract and exclude binary masks.

Manipulate digital skeletons

Visualize digital skeletons created with ImageJ's Simple Neurite Tracer plugin.

Resize, recalibrate and flip skeletons, and convert them to binary masks.

How do I install VolumeCut?

  1. Download latest VolumeCut version from the top of this page
  2. Install VolumeCut using MATLAB's "Install App" button
  3. Start VolumeCut from your Apps list.

System Requirements

Software: Hardware (recommended):
  • CPU: Intel >2GHz
  • RAM: 16Gb
  • GPU: 2Gb VRAM for volume rendering