DIMACS
DIMACS REU 2013

General Information

me
Student: Marc Aurele Gilles
Office: Hill 323
School: Rutgers University
E-mail: mtg86@scarletmail.rutgers.edu
Project: Developing a graphical interface for image analysis of z-stacks of DIC images.

Project Description

Developing a graphical interface for image analysis of z-stacks of DIC images. This software will be used by biologist to obtain a more accurate measurement of the size and amount of lipid bodies in macrophages. I will be using PyQT for the GUI and VTK (Visual Toolkit) for the 3D representation.


Weekly Log

Week 1:
This week I went through a PyQT tutorial and prepared my first project presentation.
Week 2:
I continued learning PyQT and VTK. Getting a VTK window into PyQT has been my first challenge. I made a small project to show my mentor I understood how to use VTK and PyQT.
Week 3:
I started the actual project. I ran into my first big problem: reading in a TIF stack (TIF are 2D images) to form 3D images. I did this by reading each image in a 2D array, combine them into a 3D array and display that 3D array. I used the modules libtiff and numpy to achieve this.
Week 4:
I continued working on my project. My main difficulty this week was implementing a nice-looking FFT (fourier transform), this is central to my project as it relies on the user to select volumes in the FFT.
Week 5:
Still trying to figure out why my FFT doesn't look good. Working on implementing projections and a 3D box to select volumes from my 3D data.
Week 6:
After meeting with my mentor, I have been able to solve some problems with my FFT, and after some research on the litterature, I understood more of what is happening. However there is still something wrong with the implementation of my 3D FFT.
Week 7:
After meeting with my mentor again, it doesn't seem that this FFT problem is going to be solved. We started working on another technique which doesn't involve FFT. Preparing final presentation
Week 8:
This week I developed volume widget to select the data we want to supress. I obtained the final output of my project, however the results are not what we expected and are unusable.

Presentations


Additional Information