Icy (win, mac, linux)

Icy is free and open source. Started in 2011 with the BioImage Analysis Lab at Institut Pasteur and licensed under GPLv3.

Download and Install

http://icy.bioimageanalysis.org

Basic instruction

Link to Official document, PDF

Open Z-stack

1. Create TIFF (multi-TIFF) file from JPEG serial images using FIJI/ImageJ.
   1. Drag and drop the folder containing serial images to ImageJ bar.
   2. Save as..., TIFF
2. Open the multi-TIFF file from Icy icon

Scale

1. Input pixel size (X, Y) and sectioning thickness (Z) in the window Sequence Properties Buttons Edit to edit, and Ok to save.

Volume rendering

1. Select 3D VTK from pull-down menu. Default is 2D.
2. Adjust gray line or RGB line for brightness in the window Histogram and colormap. gray or RGB can be selected by pushing the buttons in the Histogram and colormap.
3. Adjust white line for opacity in curve window.

Orthogonal planes

1. Select Blue ball icon (View 3D data in three orientations simulteneously (XY, YZ, XZ)) from pull-down menu.

Segmentation (under practicing)

1. Region Of Interest
2. Detection & Tracking
3. Processing
4. Tools

Movie

1. Tools> 3D Rotation
2. Choose Angle step
3. Play button to compute, then movie will be appeared as a new file.
4. Save the movie file. Tab Image/Sequence> Save as...