Free 3D software

 
Fiji (is just ImageJ) https://fiji.sc/
Your best friend for general image manipulation (e.g. cropping, adjusting, and orienting image stacks), editing, and basic analysis. Many many plugins to do almost anything, some quite sophisticated. Open-source, easy multi-language scripting.

Dragonfly https://dragonfly.comet.tech/
Dragonfly is my current top choice as a free replacement for Amira/Avizo. Free for non-commercial research (license on request), well-documented and extensively used, easy to get started with video tutorials. Many of the manual segmentation tools also work directly in the 3D view. Includes a convolutional neural networks Deep Learning based tools for complex segmentation. Windows and Linux only. 

Drishti https://github.com/nci/drishti
Can make amazing visualizations, including key-frames-based animations. Powerful segmentation editor (DrishtiPaint). Steep initial learning curve, but the online tutorials are helpful. Drishti Prayog (https://github.com/nci/drishti#drishti-prayog ) makes spectacular interactive touch-screen presentations.

3D Slicer https://www.slicer.org/
An "open source software platform for medical image informatics, image processing, and three-dimensional visualization...built over two decades through support from the National Institutes of Health and a worldwide developer community.” Well-developed and widely used, with extensive documentation and training tutorials. Reasonably easy to get started. 

SlicerMorph is a Slicer extension with extensive tools for 3D analysis and morphometrics (https://github.com/SlicerMorph).

Tomviz https://tomviz.org/
A "cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data. Here the full pipeline of data processing steps from reconstruction to visualization to analysis of 3D data can be presented, saved, and restored." https://tomviz.readthedocs.io/en/latest/visualization/

ITK-SNAP http://www.itksnap.org/pmwiki/pmwiki.php 
 Designed for 3D image segmentation, "emphasizes interaction and ease of use, with the bulk of the development effort dedicated to the user interface."

Microscopy Image Browser http://mib.helsinki.fi/index.html 
A "high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets."

napari https://napari.org/stable/index.html  
 A "fast, interactive viewer for multi-dimensional images in Python is a fast, interactive, multi-dimensional image viewer, with a vibrant plugin ecosystem that expands its capability to tackle various domain-specific visualization and analysis needs." Open source.

InVesalius is a free package for reconstruction of CT and MRI images. Can import DICOM or Analyze files, export files to the STL, OBJ, and PLY formats. Volume rendering, and manual or semi-automatic image segmentation. Win, Linux, Mac.
https://invesalius.github.io/ 

ImageVis3D is a new volume rendering program developed by the NIH/NIGMS Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity.  https://sci.utah.edu/software/

Seg3D is a volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing. It combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. It has a strong emphasis on manual and semi-manual segmentation, where filtered data guides the user in making decent segmentations of the data. The program is mainly intended for, but is not strictly limited to, segmentation of biological/medical data. BioMesh3D (part of SCIRun) can be used to turn segmentations into quality meshes which can be used to simulate biological processes on the segmented images. https://sci.utah.edu/software/

ilastik https://www.ilastik.org/ 
"ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.... has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection."

CDeep3M is a containerized tool, using deep learning for large-scale image segmentation tasks. It is an open source development and the software is free to use. You can run CDeep3M on your local platforms, on cloud providers, on GPU clusters or with free GPU resources on this website. https://cdeep3m.crbs.ucsd.edu/cdeep3m

MeVisLab https://www.mevislab.de/  
A "powerful, modular framework for image processing research and development with a special focus on medical imaging."

MeshLab http://www.meshlab.net/   
Famous freeware for working with surfaces. 


The Scientific Community Image Forum at https://forum.image.sc/ is a discussion site for software-oriented aspects of scientific imaging, particularly (but not limited to) image analysis, processing, acquisition, storage, and management of digital scientific images.