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3D Slicer Reference

Free reference guide: 3D Slicer Reference

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About 3D Slicer Reference

The 3D Slicer Reference is a comprehensive cheat sheet for the open-source medical image analysis platform. It covers DICOM import and database management, view layouts (Conventional, Four-Up, Dual 3D), volume rendering with presets and transfer functions, and Window/Level adjustment for CT and MRI visualization across all standard tissue windows.

The segmentation section details the full Segment Editor toolkit including Threshold, Paint/Draw, Grow from Seeds, Scissors, Margin, Smoothing, and Hollow effects. Registration workflows cover rigid, affine, B-Spline, and landmark-based methods with transform hierarchy management. Python scripting entries document slicer.util functions, mrmlScene node operations, and CLI module execution.

This reference also covers the extension ecosystem including SlicerRT for radiation therapy planning with DICOM-RT and DVH calculation, MONAILabel for AI-powered organ segmentation with active learning, and SlicerDMRI for diffusion tensor imaging. Built for radiologists, medical physicists, biomedical engineers, and clinical researchers working with CT, MRI, and PET imaging data.

Key Features

  • DICOM import workflow, study/series browsing, and scene file management (MRB/MRML)
  • Complete Segment Editor reference: Threshold, Paint, Draw, Grow from Seeds, Scissors, Margin, Smoothing, Hollow
  • Volume rendering configuration with CT/MRI presets, ROI clipping, and transfer function editing
  • Image registration methods: Rigid, Affine, B-Spline, Landmark-based with transform hardening
  • Python scripting API: slicer.util functions, mrmlScene node management, and CLI module execution
  • Extension ecosystem guide: SlicerRT, MONAILabel, SlicerIGT, SlicerDMRI, SegmentMesher
  • 3D model export formats (STL, OBJ, VTK, PLY) and Markups for distance/angle measurement
  • Searchable by category with dark mode support on desktop, tablet, and mobile devices

Frequently Asked Questions

What is 3D Slicer and what can it do?

3D Slicer is a free, open-source platform (BSD license) for medical image analysis and visualization. It supports DICOM, NIfTI, and NRRD formats, and provides tools for image segmentation, volume rendering, image registration, 3D model creation, and Python-based scripting for automation.

How do I import DICOM images into 3D Slicer?

Go to File -> Add DICOM Data, then use the DICOM Browser to import a folder of DICOM files. The browser lets you browse studies and series, load selected data as scalar volumes, and manages a local DICOM database automatically.

What segmentation tools does 3D Slicer provide?

The Segment Editor module offers Threshold (automatic by HU value), Paint/Draw (manual brushing), Grow from Seeds (seed-based region growing), Scissors (freeform cutting), Margin (expand/shrink boundaries), Smoothing (Median, Gaussian, Opening, Closing), and Hollow (shell creation for 3D printing).

How do I set up volume rendering in 3D Slicer?

Open Modules -> Volume Rendering, select a preset (CT-AAA, CT-Bone, MR-Default), adjust the Shift slider for brightness, set an ROI for clipping, and choose between GPU or CPU ray casting. The transfer function editor allows fine-tuning opacity and color mapping.

How do I use Python scripting in 3D Slicer?

Open View -> Python Console to access the interpreter. Use slicer.util.loadVolume() to load files, slicer.util.getNode() to access scene nodes, slicer.util.arrayFromVolume() to get numpy arrays, and slicer.cli.run() to execute CLI modules programmatically.

What is MONAILabel and how does it work with 3D Slicer?

MONAILabel is an NVIDIA MONAI-based extension that provides AI-powered segmentation. It uses a server-client architecture with pre-trained models for automatic organ segmentation, supports active learning workflows and DeepEdit for interactive AI-assisted segmentation, and allows custom model training.

How do I export 3D models for printing from 3D Slicer?

After segmentation, click Show 3D in the Segment Editor or go to Segmentations -> Export to models. Use the Hollow effect to create shell models, then export as STL format. The Models module lets you adjust color, opacity, and clipping before export.

Is this 3D Slicer reference free to use?

Yes, this reference is completely free with no account or download required. All content runs in your browser with zero server processing. It is part of liminfo.com's collection of free online reference tools for medical imaging and scientific computing.