Archives for July 2, 2018

REThink 2018, Week 1

For this iteration of the RETHINK Program, I believe I am going to try weekly blogs instead of daily blogs. I am fortunate enough to be working with Dr. Mark Zarella again. Here is my experience for week 1:

Monday: Believe it or not, I still had school. So I had to miss the first day. It sounds like it was very similar to the first day from 2015, where it was general on-boarding and procedures, as well as countless trips to the ID card office to try and get everyone ID cards.

Tuesday: Came in and met my partner for this year, Laurence. There was a debrief with the group, in which I was able to meet everyone who is participating this year. Laurence spoke with Dr. Mark Zarella the day before, who mentioned that one of the projects would be writing a tutorial for the current algorithms that they have working, as it seems that not many in the academic world are utilizing these algorithms. I then did a literature search to see what Mark et al have been up to. I read the following articles:

“An alternative image representation for the reduced impact of H&E staining variability”
Zarella MD, Yeoh C, Breen DE, Garcia FU
PLoS One 12(3): p. e0174489 (2017)

“A template matching model for nuclear segmentation in digital images of H&E stained slides”
Zarella MD, Breen DE, Xin W, Garcia FU
Proceedings of the 9th International Conference on Bioinformatics and Biomedical Technology, Lisbon, Portugal (2017)

“Contextual modulation revealed by optical imaging exhibits figural asymmetry in macaque V1 and V2”
Zarella MD, Ts’o DY
Eye and Brain (9): 1-12 (2017)

“Cue combination encoding via contextual modulation of V1 and V2 neurons”
Zarella MD, Ts’o DY
Eye and Brain (8): 177-193 (2016)

“Lymph node metastasis status in breast carcinoma can be predicted via image analysis of tumor histology”
Zarella MD, Breen DE, Reza MdA, Milutinovic A, Garcia FU
Anal. Quant. Cytol. Histol. 37(5): 273-285 (2015)

We then set up a meeting with Mark for Wednesday afternoon.

Wednesday: First, I met with Laurence and finished literature review. We then met with Mark over at the Drexel Medical School. He detailed his two wants:

1. A tutorial so that more people will use the algorithms in the academic world. He gave this website as an example:

2. Integration with QuPath, a (relatively) new open source program for pathology, of which there may be a way to integrate his MATLAB scripts.

Laurence took need #1, and I will be working on need #2.

I also found out they are still using the MATLAB script that I got working during my last stint in the REThink Program in 2015.

Thursday: I went over to the Neuroergonomics conference at the Bossone building, and went to the poster sessions. It was very interesting seeing this growing field, and the new devices that they have to measure EEG and fNIRS. I then used the downtime to see about getting the 2015 script running in MATLAB. It wasn’t working as expected, and for the life of me I couldn’t figure out why. I ended up downloading the new BioFormats toolbox for MATLAB. That helped, but it still wasn’t passing the image through as expected to open the viewer.

Friday: I woke up with an idea of how to solve the issue, and immediately made the chnages in MATLAB and it now runs flawlessly. We met up to discuss our Project Proposals, and then went to one of the dining commons for lunch. I tried to set up QuPath for MATLAB, and encountered an issue with the toolbox (which outputs an error and is semi-deprecated.)  I then joined the QuPath Google Group to inquire about any potential solutions to this error.