Mac

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation.

OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org

Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

NeuroMorph is a toolset designed to import, analyze, and visualize mesh models in Blender. It has been developed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, but much of its functionality can be applied to any 3D mesh. These mesh objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. 

This is a classical workflow for spot detection or blob like structures (vesicules, melanosomes,...)

Step 1 Laplacian of Gaussian to enhance spots . Paraeters= radius, about the average spot radius

Step 2 Detect minima (using Find Maxima with light background option to get minima). Parameter : Tolerance to Noise: to be tested, hard to predict. About the height of the enhanced feautures peaks