Trevor Russo, Week #6: Putting a (Binary) Mask over CMU

Awful title aside, this post, which includes last week and all progress up until today, is about my breaking free from the cycle of failure that had been 3D Modeling. Last week was a little difficult, as I spent the first few days as usual just plugging away at the modeling software. After a while I became frustrated beyond belief, and was about to lose faith in my ability to finish the project when my fellow intern, Joe, told me about someone that had also worked on 3D Modeling, named Pedro. I texted Pedro and asked if we could meet up to try out the software that he used, Agisoft Photoscan. He came down to the lab and gave me a quick tutorial, but the real breakthrough came when I showed him the Berkley Dataset I had been using. He noted that the reason the pictures weren't working was because the turntable they had been positioned on was static but the object was not. When the software, Autodesk Remake for example, attempts to reconstruct the scene, it automatically estimates the camera position and stitches together the photos based on this information. Because the actual turntable was static the entire time, the algorithm was confused. I wish this information had occurred to me long before I lost 3 weeks to faulty modeling, but I took this as a victory in itself.

Then I remembered what Venkat had told me about a possible solution, and for the first time, I decided to mask my photos. Masking is where a binary mask, which is a collection of 1s and 0s, is applied to a photo, essentially "turning on or off" the pixel in that location. After applying the mask, the photo eliminated the background. And when further plugging these new images into Autodesk Remake, it produced a solid model of the Cheez-It Box pictured below. Now the Berkeley pictures came with binary masks, and the photos that I and others will be producing won't have them, but I have been assured by Venkat that the program that will produce masks will be written separately after I leave.

 Before Masking

After Masking

  

Between that, I decided to try and take my own photos, creating a dataset for my water bottle. Unfortunately the model was lacking, and by lacking I mean lacking its middle portion. And with 2 days to go, it seems like trying again doesn't seem like the best use of my time. So, in order of priority, my tasks follow as such:

1. Write a Program that AutoWhiteBalances the pictures

2. Produce more models from the Berkley set and using my masking program mask them

3. Test out my Photo program with an actual kinect

4. Write a report so that others who use my software know what to actually do.

And that's about it. I'll write another post on Saturday on the way home, but after 6 wonderful weeks, it's somewhat surprising and saddening to know that I'm leaving a place that has been like a second home to me. I love everything about the city and the college, and hopefully I can continue here for four more years.

Other Photos:

The Water Bottle I took photos of

 A UAV about to take flight towards a goal

A King upon his Throne

Jay Swarup, Entry #4

Hey everyone,
I just finished up a few more weeks at the Ramachandran lab. During this time, I did an experiment over again. But, I finally got good results for the experiment! The experiment in which I repeated was the one in which the goal was to increase the granule size by a certain amount. After adjusting certain parameters on the granulator, I was finally able to successfully produce granules of the correct size. Now, I have been assigned to work with another graduate student. In this experiment, in which I will start tomorrow, we will measure RTD, which is the residence time distribution. But before we could start the experiment, we had to make pre-blends. Pre-blend powder is the powder that the granulator uses to make the granules. To make pre-blends, we had to measure a certain amount of each chemical, such as APAP and MCC, and then put it in the machine. The machine that mixes all of the powders together is pictured below. To clarify, the machine is in the middle of mixing the powders which is why it is rotated and not on the floor.

After the machine ends, we take the powder out and clean the machine. Unfortunately, cleaning takes up a long time and the machine runs for 30 minutes. So, making 10 batches took up a lot more time than we anticipated. But, it was worth it in the end because now we have enough powder to complete our entire experiment.
Aside from working in the lab, I have been playing sports as usual and hanging out with friends and family. Also, Dr. Venanzi visited me and we had lunch together which was very nice.

Julia Hu Entry 5 -- Last Week!

Last Friday, I finished my final week at the Fuccillo lab. During my last week, I cut one last C57 Wildtype brain and performed immune staining on it. Unfortunately, I was not able to finish off the molecular cloning project because we are having the same issue with the final step for both the hSyn-hm3D-2a-smRuby-V5-pA construct and the hSyn-ReaChr-2a-smRubyMyc-pA construct. Hopefully, Dr. Fuccillo, or Marc as I am now able to call him, and Felicia will be able to resolve the problem and complete these last two constructs for viral transfection. The three of us will keep in contact about the cloning project via email.

On Friday, our lab had a visitor named Ronnie, a student who just graduated from Brown University and is currently working at Dr. Chris Moore's neuroscience lab at Brown. Ronnie came to visit our lab to learn more about electrophysiology from our postdocs and also to see what kind of research our lab is performing. I was surprised to learn that Ronnie is diagnosed with Tourette syndrome, a neurological disorder involving repetitive movements or involuntary, unwanted sounds (for example abrupt yelling or moaning) called tics. Currently, there is no cure for this disorder, and it can last for years or even be lifelong. These symptoms of Tourette’s can be debilitating for the patient and can troublesomely interfere with his or her daily life. It really inspired me to see that someone with a neurological disorder is pursuing a career in neuroscience and that instead of allowing the disorder to overtake his life, Ronnie is actively battling against Tourette’s through the path of research.

Before I left on Friday, Marc chatted with me to do some last minute debriefing and to give me some college and life advice that I thought I would share with you guys. Regarding the college application process, Marc reminded me to not utterly stress out and that rejections from colleges are not the end of the world. One piece of life advice he mentioned that really resonated with me was that in the future, I will notice that each person has one particular quality that sticks out. For example, I will find that some people are extremely efficient while others are very hardworking and diligent. Marc explained to me that in the end, it is characteristics such as efficiency, grit and perseverance that lead to success and not necessarily ‘intelligence’ on its own. From working at the Fuccillo lab this summer, I feel that I have gained more grit and persistence from working longer hours to troubleshoot failed experiments (and to fix my mistakes), and I have learned to not give up in face of those blunders and failures. I have come to fully understand how true failure lies not in falling itself, but in being unable to pick yourself up after falling. 

It still amazes me how close I became with everyone in the lab within these 7 weeks. I even became quite close with some members of the neighboring labs. These people became not only my mentors but also my friends. When I said goodbye to all of them on Friday, they came to hug me, and it was a surprisingly emotional farewell. We plan on having a celebratory lunch later in August, so I will get to see all my lab members one more time before the school year starts.

Dinner at Zarino’s. From left to right: Andrew (undergraduate), Felicia, and Elizabeth (postdoc)

I would like to thank everyone in my lab, particularly Marc and Felicia, for allowing me to have such a great experience this summer, for teaching me so much, and for being so patient and kind to me. I would also like to thank Dr. Venanzi and Dr. Peretz for introducing me to such a wonderful research opportunity. In addition to expressing willingness to have other Peddie students in his lab in the future, Marc has also invited me to come back to the Fuccillo lab next year if I would like to return again, so perhaps I will see all my lab members again next summer. 

Me sitting in Marc’s chair

Tiffany Budiman, Entry #2, Meeting the Mice

The past two weeks, my lab partner Reem and I have been working with Sarah who is responsible for the handling the mice aspect of the protocol. Reem and I handle the mice and along with Sarah's guidance pre-condition them. It was intimidating at first but Sarah assured both Reem and I that we would be more comfortable and at ease around the animals over time. After a few days of handling them, I performed a Von Frey test on the first group of mice and taught Reem how to do it on the second group of mice. After surgery performed by Sarah, I performed a second Von Frey test on the same group of mice to see whether or not their pain threshold changed after surgery. After Von Frey testing, we condition the mice for 8 days alternating drugs every other day. On Monday I am going to watch Sarah perform surgeries on the second group of mice and continue conditioning on the first group. Reem only came in a week ago and it was nice to have someone to work with throughout my time here. I usually handle the mice myself so it was nice to have someone to talk to while working and the job gets done a lot quicker. It's also quite scary to go down to the vivarium alone especially because the room where my lab's mice is in is in a reversed day and night schedule so it's completely dark and it scared me the first time I was in there myself. (I would post some pictures but we aren't allowed to take pictures of the animals)

When I'm not busy with the mice, Sarah has also been showing me how to analyze data from the CPP and Von Frey tests. Chris, an undergrad student also showed me the Western Blot process and I did a part of it myself earlier last week. After three weeks, it feels good to be comfortable in the lab and knowing everyone who works here. I also got my picture taken for my ID that gives me access to the vivarium and I got fitted for a lab coat with my name on it that made it more "official." I also met Danny last week and he was trying to teach me how to play Pokemon.

Danny and a pokemon

Now that I'm finally settling into my routine and work in the lab, it's hard to believe I'm halfway through my time here.

Nicholas Massenburg, Entry #6, The Final Stretch Part 2

I realized in the last two weeks of my work at the Jordan-Sciutto lab that I have had barely any time to speak one on one with the namesake, Kelly, our PI. Our lab is on the larger side of about 20-25 people, and often times because there are so many projects, Kelly gets roped into grant writing or traveling to receive support on the lab's behalf. She additionally serves on the board of several science foundations, which consumes much of her time to do any lab work herself anymore. Usually the ones who grab any time with Kelly are the Lab Manager/Second PI Cagla, The Post Docs, or lucky doctoral students. But I finally got the chance to chat with her for about ten minutes, which gave me a lot of insight into the field of HIV-neuroscience research, and laboratory science as a whole.

When I have too much free time on my hands, I start to reflect on really sappy or embarrassing things, so it was only pertinent for me to begin to reflect on my opportunity this past summer. In talking with my associates over lunch, I realized many of them had none of the same opportunities as teenagers that I have had even in my freshman year, and most definitely not through EXP. They have really been surprised by my knowledge of their fields of study, largely thanks to AP Bio (and Biotech) and the reading that we had to do for EXP assignments. Because of this, I was extended an invitation to come back to the lab in the event that I am accepted to my #1 choice of college, which is UPenn. I am really happy to know that, even if I decide to work elsewhere, I have an organization already waiting with open arms for me to potentially return.

This last week will be dedicated to me shaving off some of my  poster for EXP, finalizing any results we obtained, and making sure to express gratitude for everything this lab has taught and done for me. Here's to one more week.

Nicholas Massenburg, Entry #6, The Final Stretch Part 2

I realized in the last two weeks of my work at the Jordan-Sciutto lab that I have had barely any time to speak one on one with the namesake, Kelly, our PI. Our lab is on the larger side of about 20-25 people, and often times because there are so many projects, Kelly gets roped into grant writing or traveling to receive support on the lab's behalf. She additionally serves on the board of several science foundations, which consumes much of her time to do any lab work herself anymore. Usually the ones who grab any time with Kelly are the Lab Manager/Second PI Cagla, The Post Docs, or lucky doctoral students. But I finally got the chance to chat with her for about ten minutes, which gave me a lot of insight into the field of HIV-neuroscience research, and laboratory science as a whole.

When I have too much free time on my hands, I start to reflect on really sappy or embarrassing things, so it was only pertinent for me to begin to reflect on my opportunity this past summer. In talking with my associates over lunch, I realized many of them had none of the same opportunities as teenagers that I have had even in my freshman year, and most definitely not through EXP. They have really been surprised by my knowledge of their fields of study, largely thanks to AP Bio (and Biotech) and the reading that we had to do for EXP assignments. Because of this, I was extended an invitation to come back to the lab in the event that I am accepted to my #1 choice of college, which is UPenn. I am really happy to know that, even if I decide to work elsewhere, I have an organization already waiting with open arms for me to potentially return.

This last week will be dedicated to me shaving off some of my  poster for EXP, finalizing any results we obtained, and making sure to express gratitude for everything this lab has taught and done for me. Here's to one more week.

Nicholas Massenburg, Entry # 5, The Final Stretch Part 1

I wasn't able to get to the blog this past week and a half ago, so I thought I would take this time to reflect on the last bit of my stay here.

The lab has gotten even bigger than when I first got here, and by about seven people. My lab is housed in the Dental School of UPenn (which I've come to find out is very very expensive, good thing I have no interest in Dentistry). Second and third year students, in addition to their clinic rotations, must do a supervised bio laboratory rotation under a pathology PI. This means space in the office areas has been scarce, which has stalled some of my work. The lab science portion of my studies with STC-2 has come to an end, and in these last two weeks, I will be dedicated to quantifying our obtained results using averaging algorithms on excel, as well as the Keyence microscopy machine and antibody staining. When I first arrived to the lab, I snagged one of two free computers in the office space, but now since so many other people also need the computer for work, I find that I am getting bumped from my seat very often. This has decreased the efficiency of my analysis, but is not something that has been too cumbersome.

In addition to the minimal amount of time available on each computer, other factors (of my own doing) have been slowing down the analysis. Having misread the conditions for the labeled plates we used in the experiment, I applied the wrong conditions to the wrong calculations, and when I made graphs for those calculations, the mistakes were too late. A two day project became five days as I had to start from scratch on four separate experiments. Post-doc Dan has been very polite about these setbacks, but this is his work and livelihood, so I'm a little worried that this might be interfering with his progress. He reassured me, however, that it is his job to teach me, and that I have nothing to worry about.

In our past round of lab presentations, I received acknowledgements in three separate projects because of my contributions to structure, theory, or phrasing (on the acknowledgements page, since my name is so long, you can immediately see it tucked in the middle of the listed names). I find that I have also been contributing to one of my strongest areas in public speaking and presentation. After I helped one grad student prepare for her presentation in front of her program, several other lab members have come to me to help them with their presentations. I was surprised and how lacking in public speaking skills that much of the lab is, but ultimately I am glad my assistance has helped in perfecting presentations.

To be continued on Part 2...........