luckylara / masiv

Matlab Streaming Image Viewer - a viewing and analysis platform for ultra-large 3D imaging data

MaSIV README

What does MaSIV do?

• MaSIV is an image viewer, designed for large (>100GB) 3D image datasets.
• It works by creating a downsampled stack, which is then navigated as you would a regular 3D image stack.
• However, the program pulls data from the hard disk to a cache when zoomed in, allowing all the original detail to be viewed
• Features can be added using plugins
• Works on Linux, OS X, and Windows

What kind of data can I view in MaSIV?

• In theory, MaSIV should work with any 3D image set, stored in disk in individual xy planes saved as .tif images
• MaSIV has been designed to accept data where each depth is stored in a separate tiff. A text file tells MaSIV which planes are to be grouped together into a single 3D image.
• Currently there no support for multiple channels.

Installation

• Clone the repo and add only the root MaSIV directory to the MATLAB path.
• Dependencies:
  • Image Processing Toolbox
  • Parallel Processing Toolbox
  • Statistics and Machine Learning Toolbox
  • Subpixel Registration
• Run 'masiv'

Using MaSIV

Please see the Wiki for further information and file an issue if you run into bugs or have a question.