Tuesday, October 6, 2020

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.

Thursday, September 10, 2020

3D Imaging and Modeling


300416 UE Imaging and Modeling Using MicroCT (formerly PP)  [Winter Semester only]
 
300530 UE  Imaging and visualization in developmental biology - Principles and applications, including 3D Methods [Summer Semester only] 


First class meeting is Tues. 6 Oct 2020 at 11:30.
You may attend the first meeting ONLINE through Moodle (link available soon), or IN PERSON in the Theoretical Biology Imaging Lab (UZA I, Ebene 2, Spange 3)). There is no disadvantage to attending the Vorbesprechung online instead of in person.  

For the first few weeks, we will meet ONLINE on Tuesdays, probably at 11:00 (this is still flexible). During those meetings we will plan the projects. After that students will continue with their project work on their own schedules. The course schedule is not blocked. 
 
At the end of the semester each student or group will give a short presentation of their project to the class, probably also online. 



Instructor:
Dr. Brian Metscher
Senior Scientist
Dept. of Theoretical Biology

Tel. 1 4277 56704
brian.metscher@univie.ac.at
http://homepage.univie.ac.at/brian.metscher
http://theoretical.univie.ac.at/people/metscher/



Topics will include optical and other modalities of microscopic visualization, digital imaging, and 3D methods and analysis, with particular emphasis on x-ray microtomography (microCT) and a variety of applications.

Additional topics may be covered according to students' interests.

The UE is a companion course and prerequisite to the Project Practicum (UE 300416) on microCT imaging. You may take the UE course at the same time as the PP. (You also may take the UE without the PP.)


Evaluation is based on attendance and participation (2/3), and homework (1/3). Attendance is required: two absences (excused or unexcused) will be allowed before your grade is affected.

There will be weekly homework assignments, some of which will include a written assignment to be collected in class; others will include in-class discussion or presentation. These will account for 1/3 of the final mark.


Registration:
If you are enrolled but cannot attend the first class, you must send me an email about this before the first class. Include your registered name and Matrikelnr.