Image software and starting with Fiji

In this course we will try out several software packages for manipulating, viewing, segmenting, and presenting 3D images. Top of the list are Fiji, Amira, Dragonfly, and Drishti. 

Look at this list of free 3D image software: http://microtomography.blogspot.com/2019/04/free-3d-software.html

For next week's class:   Try using Fiji (is just ImageJ):  http://fiji.sc/Fiji

First try to download and install Fiji.

And then try out some things with Fiji. You don't have to do all of the following, just start seeing what it can do.You are welcome to use the computers in our department if you don't have Fiji yourself.

a) Open an image (any picture you like; there are samples under File → Open Samples..., or you might be able to find a picture of some kind on the internet), and try some of the basic functions.  Under the Image menu, experiment with the functions in the Type, Adjust, and Lookup Tables menus.

A useful guide (for reference, not required reading):
http://imagej.nih.gov/ij/docs/menus/image.html

You might find the online documentation helpful:
http://rsb.info.nih.gov/ij/docs/

Some things to try:

Look the image histogram (under Analyze → Histogram)
Image → Adjust  → Brightness/Contrast...
               "             → Window/Level...
               "             → Color Balance...
               "             → Threshold...

Image  → Show Info...     (and try this with a picture from your phone)
      "    → Properties
      "    → Lookup tables →
      "    → Type          (what do these types mean?)

Process → Smooth
      "      → Sharpen
      "      → Filters → Gaussian blur

and anything else you feel like trying.


b) Try opening this image stack, from a microCT scan of a salamander larva (Ambystoma maculatum; the "PTA" in the filename stands for phosphotungstic acid, a stain that gives x-ray contrast to soft tissues.)
http://homepage.univie.ac.at/brian.metscher/Amaculatum_PTA_8bit.zip

Under the Image → Stacks menu, try the Orthogonal Views, Reslice, and Z-Project functions.
With the stack open, try the 3D Viewer, and the Volume Viewer (under the Plugins menu). 

Try other stuff if you feel like it.