Archives for July 27, 2015

REThink 2015 Day 20- Terrible PATCO commute, Posters, MATLAB Functions

So this morning was perhaps the worst PATCO commute, due to 2 broken down trains, and the fact that there’s only one track to get across the Benjamin Franklin Bridge. We were delayed for 47 minutes, so I ended up being super late this morning. As per usual, we did our weekly check-in, and I reported about my current progress (see previous post).

We started talking about our Poster Session. If you’re interested in coming out and seeing the work that everyone has done, here’s the information:

Room 326 at the Science Center (3401 Market Street / the Excite Center) on Wed 8/12 at 2pm.

We then talked about the data for each of our projects. Here’s what I wrote:


The input data of my project is ImageScope files, from the Aperio ImageScope slides. The slides are stained using Hematoxylin and Eosin stain (H&E). The slides were made daily

The output data of my project is .mat files, to be analyzed using MATLAB. I will be using the “scatter3” function in MATLAB to analyzed the HSV colorspace of the files.

Data Type

The data type is descriptor  ‘classidx’ and ‘centroid’ variables in each output file to assign a centroid value to each.  The data contains centroid values for nuclei, the centroid values for cytoplasm, the centroid values for stroma and the centroid values of white space.  There are 30 files that contain this information, so I will have 120 data points, 30 files times 4 classes per file.

What are some questions about the data?

Are the nuclei (cytoplasm, stroma, whitespace) always within a certain color space?

Are the variations in slides due to region, preparation, or analysis?


This afternoon, I did a bit of MATLAB and just basic matrix research, as that seems to be how I need to analyze this data.


That’s basically what I’m working with now. Let’s hope PATCO doesn’t let me down on my commute home!