Revision as of 17:59, 16 June 2016

Comparing Two Models of HMPAO Uptake in the Lungs

Benchmarks

1. Become familiar with MatLab syntax by creating a Computed Tomography (CT) program

2. Create a Graphical User Interface (GUI) to simulate a CT scan

3. Create GUI to simulate forward model of a Single Photon Emission CT (SPECT) scan (with and without noise)

4. Improve SPECT GUI to estimate parameters of the forward model, given the concentration of radioactive material put into the system and output of the noisy lung

5. Determine whether the parameters given by a compartmental model of HMPAO uptake in the lung are reliable

6. Answer the question: Is a Compartmental Model Sufficient to Reliably Estimate Key Physiological Parameters?

Weekly Log

Week 1 (5/31 - 6/3)

- Met with Dr. Clough

   - Discussed scope of project
   - Learned basics of CT, SPECT, and PET scans (projections, Radon transform, Inverse Radon transform, reconstruction)
   - Defined benchmarks for the summer

{ Next meeting Tuesday 6/7 with Dr. Clough and Graduate student(s)}

- Attended Dr. Factor's talk on basics of research

   - Using the tools you have
   - Thoughtful consideration of a problem and solutions
   - Know what you don't know ==> develop a strategy to figure it out
   - Find out what is already known (do you need a new algorithm?)
   - Break the problem down into manageable pieces
   - Know your audience
   

- Conducted background research on CT scans

   - How they have improved (greater efficiency and effectiveness)
   - Confirmed understanding of basics given by Dr. Clough
   

- Wrote preliminary MatLab programs

   - Created image to be scanned
   - Calculated projection image (Radon transform as well as individual projections)
   - Reconstructed image (Inverse radon transform)
   

- Researched basic GUI construction

For next week  : Begin constructing GUI for preliminary CT simulation

Week 2 (6/6 - 6/10)

- Formatted and finished basic CT GUI

   - Fixed image loading issue 
   - Researched solutions for using two axes in one GUI
   - Enhanced GUI (with help from Tony)

- Met with Dr. Clough

   - Introduced to the VA Hospital
   - Toured the lab (CT and SPECT imaging equipment)
   - Introduced to Katherine and Anthony (heretofore referred to as Katie and Tony)
   - Redefined benchmarks for the summer

{ Dr. Clough out of town next Monday-Thursday }

- Watched rat lung experiment measuring mitochondrial productivity before and after the addition of an uncoupler

- Attended Dr. Brylow's talk on basics of research presentation and paper writing

   - What goes into a "good" research talk?
         *Features*
         - Why is your project 'important', 'interesting', and 'hard'?
         - What did YOU do to solve/make progress towards a solution to the problem?
         - Why should they care? (What is the application? ==> sometimes requires creativity)
  
   - What makes a "good" research paper?
         - Answer all the same questions as above
         - Tell the story of the research (X3)
           *tell them what you're going to tell them (Intro)
           *tell them (Content)
           *tell them what you told them (Summary)
         - Tell them why your research is different (Related/Prior work)
   

- Constructed GUI for SPECT forward problem

   - Select data set (in .txt format)
   - Enter values for variables to graph lung curve
   - Save a copy of the GUI interface (including which data file used, all variables and output graph) to pdf

For next week  : Begin work on inverse SPECT GUI

Week 3 (6/13 - 6/17)

- Debugged GUI for SPECT forward problem

   - Emailed Katie code for additional testing

- Formatted and finished SPECT Lung Simulator

   - Fixed lung curve calculation issue 
   - Translated poisson noise code from Ben (C to MatLab)
   - Researched use of Gaussian noise
   - Created additional option of saving simulated lung data points

- Attended Dr. Brylow's presentation on Responsible Conduct of Research

   - OBLIGATIONS
     1) to honor the trust that colleagues place in us
     2) to ourselves and our future careers
     3) to the public
   
   I: ethical treatment of data
      A- how data was obtained
      B- double-blind trials
      C- validated survey
   II: authorship, credit, and plagiarism
      A- fabrication, falsification, and plagiarism
   III: human participants and animal subjects
      A- Common Rule
      B- informed consent
      C- Institutional Research Boards (IRBs)
   IV: intellectual property (who owns your work?)
   V: conflicts of interest and professional standards
      --follow your work to its end

- Conducted background research on HMPAO studies with rats and ALI

- Attended Dr. Corliss' presentation on the basics of LaTeX

   - How to access
   - Basic points of TeX syntax
   - Brief history of TeX and why Knuth created the processor

{ Beginning to work with LaTeX creating research paper }

For next week  :

Week 4 (6/20 - 6/24)

Week 5 (6/27 - 7/1)

Week 6 (7/4 - 7/8)

Week 7 (7/11 - 7/15)

Week 8 (7/18 - 7/22)

Week 9 (7/25 - 7/29)

Week 10 (8/1 - 8/5)

Personal Information

Kim is studying Mathematics at Lindenwood University in Saint Charles, MO.