Wednesday, August 24, 2011

Day 33

          I got to work early and I added presenter's notes to the slide show. After the staff meeting, I had to fill out a survey of how my experiences were this summer. Afterwards, Halle and I walked over to the color science building to participate in an experiment. They had us look at 60 images and circles areas in the images that were important then number those circles by level of importance. It was a nice, simple activity for the morning. After the experiment I talked with Dr, Berns who is the head of the color science program about the program. He gave me a tour of facility. The equipment was pretty nice and the work was compelling. He also highly recommended the imaging program as an undergrad then going into color science for grad school.
          In the afternoon Elaine and I ran through the powerpoint again. It definitely got a lot better and I don't think that we will go over during the final presentation. I'm kind of looking forward to just presenting. Hopefully everything will go well for everyone.

Monday, August 22, 2011

Day 32

        Today felt long. I brought in some cupcakes this morning from a family party that we had over the weekend. Those made the morning slightly more exciting. Elaine and I went up to see Joe Pow this morning to check over our powerpoint. He warned about going over the 20 minutes which is my biggest concern at the moment. Hopefully we'll get through it all right on thursday.
       Elaine and I began to work on our poster that summarizes our research and the capabilities of the new NMR machine. It is about half way done and it is looking very professional. I am excited at the thought that it will be hung up in the lab that we have been working at all summer. I'll probably work on it some more tonight and we can show Dr. Hornak tomorrow morning.
      Lastly, Elaine and I also did the first run through of our presentation by ourselves today. We both have plenty of room for improvement in the area of clarity of our words. A lot of the theories that we are presenting are very delicate so it's important that our language is precise and accurate. Again, I'm hoping that this will work out for thursday.

Friday, August 19, 2011

Day 31

           Today was another slightly boring day because all Elaine and I had to work on was our powerpoint. We keep adding slides to explain concepts, variables, and theories we introduced previously. However these explanations are going to take some time so we've had to cut back on some other slides. All in all it's coming along. I think that everything in regards to changing NMR variables to create a better picture is going be kind of dry; but when we actually start showing NMR images, I think we'll pick up some attention.

Thursday, August 18, 2011

Day 30

          Today we asked Joe about the theory part of our presentation. He was very helpful in clarifying the terms and concepts that we would be covering in our presentation. Elaine and I worked on clarifying these concepts. I got a really good idea of where our presentation is going thanks to the theory work Elaine and I put into it today.
         We showed Dr. Hornak our presentation for the first time at the end of the day. He gave us some really good suggestions about re-wording some areas and completely avoiding concepts with over-complicated explanations. Dr. Hornak also said that Elaine and I could make a poster presenting the work we have been doing over the summer and also showing off the capabilities of the new NMR machine. This task would be for next week if we have extra time after we have finalized our presentation.

Day 29

         Today we got some more images done for our powerpoint. Elaine brought in more plants that we needed to image with the optimal microscope. So I went right to work on those. Afterwards I put them in our powerpoint. This is a lengthy process because the microscope only has a broad enough view to image a small section of a plant stem. This problem translates into me carefully overlapping many images of the same plant to get the entire stem. In addition to that we also ran slice thickness scans on one of the plants. However the signal was so low in these images once we countered the automatic intensity scaling feature that these images were useless due to their darkness.
         We spent most of the day doing these things so we weren't able to do the theory part of our presentation. That is tomorrow's task...

Tuesday, August 16, 2011

Day 28

            This morning Elaine and I continued to work on our powerpoint. We're also trying to nail down the title for our presentation. It's a little harder than it may seem. We also created a list of everything that has to get done for our presentation.
            A student came by who was interested in the imaging science program so we got to tell her what we've been doing all summer. In addition Bethany paid for all of the interns to come to lunch with her. It was a lot of fun.
            In the afternoon Elaine and I merged what we had both been doing separately with the powerpoint. We're making progress. We're also going to retake some microscopic images as well as a few NMR images. This should give all the images we need; but we still have to spend a lot of time on the first part of our presentation in which we describe the science and theory behind MRI imaging.

Monday, August 15, 2011

Day 27

            Today was the undergraduate research symposium . In addition Dr. Hornak wasn't here so Elaine and I had free reigns for the day. We watched a couple presentations by the undergrads. They were actually pretty engaging. There was also a free catered Chinese lunch = good deal.
            In addition to that we got to go on the roof of the imaging science building. There was an experiment being set up. A plane would fly over the roof with a camera underneath and take notice of a bunch of crates that were evenly spaced. I don't actually know the point of this but we did get to help set up. Most of the interns also came back later when the plane was supposed to be flying over. After waiting an hour or so the plane still hadn't flown over so we just left. We later found out that the plane had actually flown over several times and none of us had noticed. I'm not upset though, the roof was awesome, plane or no plane. Good day.

Day 26

             Today Elaine and I spent a lot of time on very few things. We were working with the graphs for our variables for T1 and T2. We were working on creating a line of best fit for both of the graphs. In addition Dr. Hornak was showing us to  to make them look more visually up to par.
               In addition we also to the images for our slice thickness variable. This has turned into a lengthy process because instead of use converting the image to a jpeg, we also have to record signal averages and counteract the signal scaling feature within the program. So we're now ready to create a graph for those signal values and create a slide with the corresponding pictures.

Thursday, August 11, 2011

Day 25

           Today was a day full of progress. Not only was there indeed an automatic scaling feature in the NMR program, but Dr. Hornak was also able to find a way to counteract it affects. So Elaine and I were able to change the scans we had taken the day before to represent their true intensities. This made the data comparable, and we were able to graph it. There is still some margin of error in the graphs so we did some of the images over again at the end of the day.
           All the interns got to go to the grill-out for undergraduates who conducted research over the summer.  That was pretty fun except it took them a while to serve all the people that had come.
           Elaine and I also spent some time on the powerpoint. I did comparison slides showing the cross-sectional image of a plant under a microscope and the corresponding NMR image of that plant. So good data and good results basically equaled a good day.

Wednesday, August 10, 2011

Day 24

           Elaine and I got right to work with the NMR machine so it didn't have time to break on us. The images I took with the older NMR  were not very good. I say this because if you change a certain variable on each image and write down the intensity if the same pixel on each image, those intensities should form a exponential decay or loss if you graph them. However, the results I got with the older NMR machine were pretty much gibberish. So we started re-taking those images to get the proper graphs. Unfortunately after spending the morning taking images and plotting the points, those graphs were also gibberish.
          Dr. Hornak deduced that there must be an automatic scaling feature to the program which makes comparing the intensities of various images to each other nearly impossible. So when we left at the end of the day, Dr. Hornak was working on trying to find someone who might know how to turn off this feature that we think exists.

Day 23

          I caught Elaine up to speed on everything she had missed last week. We both went right down to the NMR machine in the basement with Dr. Hornak. We were excited to use it since it had been down for a decent amount of time. So of course we repeatedly got a warning message after two minutes of use. This error translated into yet another day we couldn't use the NMR. On an up note is was fixed at the end of the day.
          Elaine and I didn't get much done because almost everything we need to do involves the NMR. So we worked through our powerpoint some more instead. Dr. Hornak also set a meeting for me to talk with Dr. Smith who is a polymer chemist. I'm thinking about majoring in polymer chemistry so it was interesting to hear about the equipment in his lab and some basic theories. His main message though was to get a solid foundation in undergraduate school (major in chemistry) then specialize in polymers. So despite not being able to use the NMR, a little learning still occurred.  

Tuesday, August 9, 2011

Day 22

              I got in early and began working on my blog. After the staff meeting, I spent some time organizing a powerpoint slide. I took a dozen NMR images of the same fish that were taken at various spot at sequential spots along its body. I then organized them so it showed the cross sectional images of the fish every millimeter starting at the the tail and going all the way up to the top of the head. I must say, it looked pretty neat.  
               Soon enough, we all left for the field trip. We went to Amiel's for lunch and got subs. The food was pretty good. Once we got to Xerox, we watched a video about how the company was expanding its products. A few of the researchers that were making the discoveries for these new expansions gave us presentation about their work. Some of their work was detecting lit cigarettes at gas stations, creating security features for documents (uv marks, gloss, etc) as well as personalized, instructional medical videos for patients. That was the most interesting part to me. We got a tour of the manufacturing facility for a $600,000 printer afterwards.
              When I got back to RIT, Joe said the NMR machine was back up and running again. So hopefully, Elaine and I can begin taking images on monday...

Friday, August 5, 2011

Day 21

            I came in early to convert the NMR images I took with Dr. Hornak the other day to jpegs. But when I went downstairs, all three of my labs were caution taped. I guess those rooms were due for cleaning because all the furniture was in the hallways. So I went upstairs and wrote my blog instead.
           After the staff meeting, I worked on two graphs that were supposed to tell me the T1 and T2 values for the sample I had imaged. In addition to that, I also tried to convert my images because the lab was open after and  hour or two. Only one of my graphs was conclusive the other was completely messed up. The old NMR machine is not producing the best data that can be used for graphs.
           Then I was having problems with converting the images. Turns out I was using the wrong version of IDL. But the second Dr. Hornak left, of course, there were problems again. I was a little frustrated, so I just stopped and went to the grill-out. That turned out to be a lot of fun despite the fact that several interns are gone on vacation. We managed to get a Frisbee stuck in a tree. Matt climbed the tree to try and get it out, but was unsuccessful.
           I talked to Dr. Hornak after lunch about the pictures. He figured out that the picture I was trying to convert had been corrupted somehow and that's why it wasn't working. After that I was finally able to convert all the pictures with no problems. Later in the afternoon, the engineer came to fix the NMR machine. He brought all kinds of equipment and was hooking it up and running tests and fixing current and other things I wasn't quite following. But I had to leave while he was still working so I'm looking forward to see how thing's are coming...

Thursday, August 4, 2011

Day 20

         Today until the rest of the week Elaine is on vacation so it's been kind of quiet. I talked to Dr. Hornak after the staff meeting about Elaine and I's idea about the final presentation regarding optimizing NMR signal. He seemed to like it and he just encouraged me to do a section at the end with implications in which Elaine and I would cover things that could be imaged with an NMR tube and some of the pictures we have taken thus far (plant stems, fish, etc..).
         He told me ways to get the variables that would influence image quality. So now I have a rough outline of the things I need to do to get the right variables for the best image possible. I think we finally managed to pin down a project this time, so I'm pretty excited.
          In te afternoon Dr. Hornak and I went to the college of science to continue to work out the kinks with the older NMR machine. We ran into a few more problems. The main issue was that a line of high intensity signal kept appearing in some of the images that should not be there. However, we were able to take some good images that we can use to calculate some of the variables. My next task is converting those images to Jpeg and creating and excel graph with signal intensity and TR values.

Wednesday, August 3, 2011

Day 19

         Today Elaine and I managed to get a lot done. In the morning we began working on our powerpoint. Because the NMR machine is still down, we have abandoned the idea of creating a presentation that focuses on the dehydration of plants and the effects of certain liquids. So now we think we'll give a presentation on how to optimize NMR image quality by showing the effects of certain variables. Such variables include slice thickness, magnitude of the magnetic field, sample relaxation time, as well as a few more technical variables.
          We began working on our powerpoint. We wrote a few slides that had to do with the basic science principles behind NMR imaging. In the afternoon we went back over to the college of science to work on the parameters for the old NMR. After two hours Dr. Hornak was able to get it working pretty well. This was very uplifting to us.
          That was pretty much it for the day. It doesn't sound like a lot, but it felt like we made a lot of progress with our final presentation.

Tuesday, August 2, 2011

Day 18

        Elaine and I scheduled time to use the old NMR machine today. However Dr. Hornak sent us an email this morning that we had actually scheduled it on sunday. Those tend to be the effects of friday afternoons; thankfully there was still time left in the afternoon that we were able to reserve.
        As part of the staff meeting, Elaine and I took all the interns down to our lab and showed them what we have be doing the past few weeks. I think that went pretty well. As I was talking about our progress I realized that we have learned a ton in the past few weeks and have taken close to 100 images between the NMR and the microscope.
          After that we went up to Dr. Hornak's office. He was in a bit of a panic because we only have a few weeks left, our NMR machine is down, the old NMR is not looking too promising, and he wants us to still have a good time and learn in spite of that all. So he introduced us to a mini MRI machine that we could try to use. Our currently broken machine had a magnetic field of 11.6 tesla. This mini machine has a magnetic field of 5 x 10 ^ -5 tesla. As you can imagine, this is a huge difference that means there is much less signal and a lot of background "noise" (interference). Consequently this machine which is about one cubic foot is incredibly sensitive to metal. We spent the morning with a compass trying to figure out where there was the least pull from surrounding metal objects (these objects interfere with the signal). The best spot turned out to be the front lawn.
             We tryed to set up the machine in Dr. Hornak's office first, but the signal was very poor. We are not sure if it's going to work out; but one of the up sides is that we can fit sample in it with a 5 cm diameter which opens up many more doors than 4.5 mm.
            In the afternoon, we spent more time trying to set up the imaging program on the old NMR machine. We got an image that was very distorted compared to the other NMR. Dr. Hornak was able to center it and make it the right proportions. But then a gradient overload caused the system crash. So we might very well be back to square one...

Monday, August 1, 2011

Day 17

        Friday was a bit of a slow day. Elaine and I didn't do mch in the morning. We were scheduled to use the 12-year-old NMR machine in the college of science in the afternoon so we did print out the program parameters for the machine we have been using in order to copy them into the other system.
       We had our picnic, grill-out for lunch. Prati brought gnome bowling which is surprising harder than it would see. We also spent some quality time playing frisbee. 
       After lunch Dr. Hornak took Elaine and I to the older NMR machine. The normal probe for the machine does readings for spectroscopy. The one we've been using allows a person to use the machine for imaging purposes. This means that whenever we use the older machine we have uninstall the spectroscopy probe, install the imaging probe and put the other one back when we're done. This process requires us to disconnect about 10 cords, take out the probe from the bottom of the machine, insert a new one and reconnect the cords.
        We spent time trying to copy the imaging program, however this was not very successful. The program is a much older version on the other NMR so a lot of the parameters did not transfer properly. We spent a lot of time troubleshoting but were not very successful.

Friday, July 29, 2011

Day 16

         Thursday morning I got up to speed with my blogs. We all had a staff meeting in Kelsey's lab because the reading room was being cleaned. I had no complaints because her room is decked out in very comfy couches and furniture.
          After that, I participated in the experiment for visual perception that Liz and Prati had set up. Essentially, they tracked my eye movement as I watched a soundless episode of Jeopardy with commercials. It was a little hard to follow without the sound, but I found that I was paying a lot more attention to facial expressions. At the end they did tell me the purpose of the experiment but I don't think that I can reveal it; I will say this though, it's really interesting.
          Elaine and I went down to our lab and checked on the plants that we had soaked in various solutions. The plant soaked in pure alcohol was completely dead. Everything else was still upright and appeared to be reasonably healthy. A chemistry grad student had signed up to use the NMR machine in the morning so we couldn't image any of our plants.
          At 12:20 we watched the liquid helium refill for the machine for an hour. It was fun to see because the machine was emitting clouds of the liquid helium. However, at that time, we also found out that there had been a problem with the machine in the morning. It was not producing the proper results so Dr. Hornak put our test sample in the machine. This is the one with the capulary tubes; I have a picture posted of it in the first few days of my blog. Instead of producing an image with many little circles in one big circle, the image was a dark rectangle. Dr. Hornak said it could be a little problem in which it might be fixed in a few days or a more serious problem in which it might take a few weeks to fix. After consulting with some people in the afternnon, he realized that it was a serious problem.
           This basically means Elaine and I have also run into a problem. There is a 12-year-old NMR machine in the college of Science which we signed up to use for two hours on friday. The problem is that the imaging part of the machine has not be programmed on it. So Dr. Hornak is going to save the program to a thumb drive and copy it to this older machine. If that machine doesn't produce good images, we may have a very big problem. All of our research is dependent on using this machine and since we don't have any of the images for our final project, we're in a bit a sticky situation. Hopefully everything will work out.

Thursday, July 28, 2011

Day 15

          I missed tuesday so that I could see Alfred University. It has the only glass engineering program in the whole country there, and I found it to be a very interesting degree. As it turned out, Elaine didn't come to work tuesday either because of a virus, so nothing really got done on tuesday.
          However Wednesday is a different story. Elaine and I worked with the plants we bought last week. We set them up so that some will be dehydrated, some will be over-wated, some will be a control group, and others are being put in various liquids (distilled water, salt water, mountain dew, alcohol, etc). After that we  imaged a healthy plant with both the NMR and the microscope. We are going to use these images as a comparison to the end results of the other plants. I hope this yields some interesting results.
           There was a free pizza lunch today with popcorn if you stayed to watch an educational movie. Most of the interns took advantage of this offer. The movie was interesting; it focused on ways to make a great presentation by using simple powerpoints.
           After lunch, Elaine participated in the visual perception experiment that Prati and Liz are doing while I hung around their lab. Because I forgot to wear contacts, I'll participate on thursday. During that waiting time though, I was introduced the game angry birds which I now find myself highly addicted to. After that Elaine and I talked through some ideas for our final project and presentation. That date is coming up fast and we're trying to begin to crack down on everything...

Monday, July 25, 2011

Day 14

           Well, I got in early today again to start research for our plant comparison. I made a chart of the plants Elaine and I have imaged with the NMR and the microscope. The hope is that similarities in the characteristics of the plants (annual, pereneial, amount of sunlight, needed water amount,etc) will correlate with the NMR images of the plant. For example, plants that are fruit bearing may have a ring of high hydrogen concentration around the edge of the stem.
           After the staff meeting I figured out how to convert the pictures taken with the microscope to jpegs so they can be viewed on other computers. I also continued to research plant characteristics. At 10:15, everyone met in the gallery (the interns and some undergrads). We took a tour of Rochester Precision Optics. One of the best parts was that RIT rented a party bus to transport us and we got to play games on the way there. The tour was pretty interesting. There was tons of machinary in the building. Also many of the rooms were pretty loud so I was curious as the whether engineers lost their hearing faster than most people. However, I'm sure they could probably figure a way to make a super advanced hearing aid. Anyways.....we all went to pizza hut for lunch. That was also a lot of fun. Ed and I were strategizing on how long to wait to get the best food in the buffet line. Out methods worked because our food was the freshest. 
          When we got back to RIT, Elaine and I contiued to work on our plant samples. However, the research was not as conclusive as I had hoped. So we went to talk to Dr. Hornak about our (lack of) results. He is suggesting that we do a study on how the NMR picture changes as we deprive a plant of water, or if we freeze it, or if we put chemicals in it. Because all of this testing requires plants, Elaine and I drove to a local plant store and bought some plants that we could use to experiment on. So that was pretty much it for today. Not bad for a monday.

Friday, July 22, 2011

Day 13

          Today was a pretty slow day. Elaine and I collected more plant samples from around campus this morning and imaged them using NMR and the microscope. After that we went to Jason and Matt's lab to see their project. As I understand it, they are further developing interactive technology to help people learn about the the sun. Next came our weekly grill-out! I was a lot of fun. Aside from eating a lot of great food, we played apples to apples and frisbee together. This afternoon, we are watching Dr. Hornak's grad student give her official research talk. We are also working on improving picture quality form our NMR scans once again. So it was a mildly boring work day but the grill out certainly amped things up a bit. TGIF...

Thursday, July 21, 2011

Day 12

             Today turned out to be one of the best days yet! First we drove over to the NTID part of campus (way too hot to walk). We went to one of their labs and got permission to borrow their microscope with a digital camera. Elaine and I spent the morning setting up the microscope to the camera and the computer, and we had time to take many photos. The images came out gorgeous; they were clear, detailed, and the right size.  After lunch we imaged with the NMR the tree branches we had photographed earlier. The quality was significantly poorer in comparison with the microscope photos. But then we imaged a fish we had soaked in copper sulfate overnight. Those images turned out relatively well. At the end of the day, we converted all of the scans we had run this week into jpeg format. All in all, a very successful day.

Wednesday, July 20, 2011

Day 11

          I came in a little early yet again today. I had bought some fish last night to image so I set those up in one of the labs in the basement. I also spent some time this morning learning how to use Gimp to alter our imaged pictures. During the staff meeting today, we all went to see Alex Smith's lab. He is working on building some special computer. It certainly sounds interesting, but I didn't really understand too many of the technicalities about it.
         Then Elaine and I went down to our lab and spent some time imaging with the NMR machine. It must not have been all that exciting because I actually remember nothing about it. At around 11 Halle and I left to go to Mercy. She went to see her counselor, and I had my last day at jewelry camp. It was tons of fun and there was ice-cream as a sending away. When I got back, Elaine and I spent our time imaging a fish. None of the pictures are good; they're all just blobs. It's getting kind of frustrating because we seem to keep coming up short.
          Also Elaine decided to make a list of movies that I should watch. I never know what she is talking about when she frequently makes movie references. So at least I have some fun homework. Tomorrow morning we are scheduled to use the microscope in the NTID part of campus so I'm looking forward to that...

Tuesday, July 19, 2011

Day 10

          Today was another short day. I started early again, and as a result, have almost finished reading Dr. Hornak's online book. Then we had a breakfast during this morning's meeting. Prati wanted all of us to eat the muffins that she had burnt. She said they weren't half bad, so I asked her if she had had one...the answer? It made us all laugh.
          Then Elaine and I went down to the lab. We continued to scan developing seeds in the MRI tubes. After that we went outside and cut some small tree branches that would fit in the NMR tubes. We also brought some copper sulfate solution to but the branches in. The idea being that it will increase signal and therefore create a better picture. We went back to the lab and checked on the internet the names of the trees from which we had taken the branches.
          Then the best part of the day was jewelry camp. The kids I'm working with are absolutely adorable. Not a single dull moment.
            I got back to RIT and caught up with Elaine. It seems that not much occurred while I was gone. So now I'm trying to learn how to use Dimp because Dr. Hornak didn't think that the pictures altered on iphoto were that great. So all in all, not a bad day.

Monday, July 18, 2011

Day 9

          I came in early today because I have to leave from 11-4 today, tomorrow, and wednesday to teach a jewelry course at my school. Early this morning, I went to the computer lab and worked on improving the quality of some of our scans with iphoto. I also read more of Dr. Hornak's online book about MRI.
         After the morning meeting, Dr. Hornak's same grad student gave us her revised presentation from last week. She improved significantly, and once she works out a few more little kinks, she should be ready to give her talk. Then Elaine and I went down to the lab and we ran scans on the seeds that we are growing in the test tubes. They are developing well. We also ran scans on a maple branch, raspberry bush branch, and a celery stalk. Many of our images are poor quality and Dr. Hornak is giving us recommendations to improve the quality. Hopefully these techniques will work.
         I left to go to jewelry camp and that was a blast! The kids were great and pretty talented. Once I got back, I found Elaine and she has updated me on what happened today. For the rest of the day I'm going to continue to  work on picture contrast with iphoto and I might go down to the lab to see if there are any more samples to scan.

Friday, July 15, 2011

Day 8

         I saw the midnight premiere of Harry Potter last night, so I have been pretty tired today. This morning we went down to the lab and spent the morning trying to figure out the default slice thickness of the NMR machine. After several hours, we figured out that it is about 1.3mm. This means that all the images taken have been a visualization of a particular 1.3mm of the sample.
        Many of us were so tired today that we didn't bother walking to global village for lunch. So we just had a picnic under the pine trees outside of the imaging science building.
        After lunch, Elaine and I did a lot of scans on a fish and a ghost squid. Each scan takes about 4.5 minutes so there is a lot of waiting involved. But we passed the time by listening and singing to music. Lastly, we went for a quick walk around campus to find possible plant stems to image. So the day is over and I'm really excited for the weekend.

Day 7

           To start the day, Elaine and I listened to a grad student practice her talk on research relating to the field of MRI. She was nervous, but what she had to say was very interesting. We made suggestion for her to improve the conclusion to make it have more pizzazz.
         We took more images of various plants and we finally got to image our fish. The platns turned out surprisingly well. And our fish wasn't producing very good imges at first then we got two really great ones. We would never have created them if Dr. Hornak hadn't showed us how to move the image slice up or down on the sample. Afterwards we finally converted all of the images we had taken with the NMR to JPEG's which means we could see the images in much higher definition.
       The high point of the day was definitely our cook-out at lunch. We all brought in food and supplies so it was like a miny potluck. Everyone got a chance to play bocee ball and ladder ball. Then the boys cooked out hots and hamburgers. I had the prestigious job of putting the burgers on the grill; I almost dropped one through the grates of the grill, but I saved it. Tomorrow's friday, can't wait for the weekend1 

Thursday, July 14, 2011

Day 6

        Tomorrow we are having a team-building lunch. Joe Pow, Bob Callens, and Bethany Choate have arranged to get us a grill and we have divided up food to bring between all the interns. I'm really looking forward to it because we'll have music, kan jam, and gnome bowling as well.
microscope that took pictures
        This morning Elaine and I planted seeds in the NMR tubes. Our hope is that they will grow and we will be able image them with the NMR machine to see their internal growth. Dr. Hornak walked us over to the college of science to use a microscope that had a camera hooked up to a computer. We were hoping to take digital photos of the stems we NMR'ed yesterday so that we could compare the two images. However the magnification of the microscope was too strong for what we needed. Dr. Hornak is looking into whether the National Technical Institute for the Deaf on the other side of campus has a photographic microscope with a lesser magnification.

Seeds we planted in the NMR tubes
       This afternoon we continued to image more plants and insects. We are finding that the plants produce nice images where as the insects mostly create a blob. In the afternoon we watched a speaker present about new scanning methods for biomedical imaging. All in all, a good day. It's just that it's getting harder to find samples to image due to the tiny size of the NMR tubes.

Wednesday, July 13, 2011

Day 5

         Dr. Hornak had a meetong this morning so Elaine and I were on our own to collect samples for the NMR tubes. It's pretty hard to find samples that fit in the tubes because the diameters are less than half a centimeter wide. Which means that most of our samples were bugs, plants, seeds, and one tiny fish.  
        We went to see Kelsey's lab on the third floor. She is working with the freshman project of the imaging science class. It's half a dome and an object is placed in the center of it. There are cameras set up in spots throughout the dome so that they take pictures of the object from different angles. After that we, went back down to our lab and started imaging some of the samples we had collected with the NMR machine. We imaged the cross section of a chive, a string bean, plant stem, a tiny snail, and a tiny worm. Of all the images the chive and the plant stem were the most interesting. The snail and the worm just created a round blob. We used several different techniques to improve the picture quality. Unfortunately, one process (creating a thicker cross section) did not work. And the other technique, which was to wait longer inbetween scans (there are a total of 256 scans to get one image), made the original image twice as defined but the time it took to image the picture went from .5 minutes to 4.5 minutes.
         We are still brainstorming for the final project because the tadpoles are too big to fit in the NMR tubes. But it was a good day because we really got right into the imaging.

Monday, July 11, 2011

Day 4

          Today was a pretty easy-going sort of day. When we all assembled in the reading room this morning and shared what each of us had done so far and our project for the summer. All of the groups had really interesting  tasks that ranged from building a intense computer to finding the exact day of a particular planetary alignment to determining the elasticity of paper without destroying it, and several other projects.          
Me cleaning test tubes
         Then Elaine and I went to Dr. Hornak's office and spent a little bit more time learning about the science of MRI. Each day that we spend going over it, the more comfortable I get with the material. Soon I really hope to have a decent understanding of the basics of MRI. After that we walked over to the college of science and picked up disposable plastic aprons and NMR tubes that needed to be cleaned. Then we spent most of the afternoon cleaning all those hundreds of tubes. After that we discussed possible things to image for the final project. We came up the idea to image a seed every day as it grows or the growth of a polliwog. The MRI image would show how much it develops in a day and over a longer period of time. I came up with a reverse idea: to watch the decay of a small insect, plant, or polliwog. If you may recall from an earlier blog the MRI measures the intensity of hydrogen regions. So decay imaging would show which parts of the object dry up or decompose first.
Elaine cleaning test tubes
          At the end of the day, we went to two of the ponds on campus and saw little fish, but no tadpoles. I do have a doubt as to whether a tadpole will actually fit in an NMR tube, which we will find out soon enough I'm sure. I'm starting to get really excited now about our project and I hope we will end up getting some really neat images.

Friday, July 8, 2011

Day 3

            Today turned into an unusual sort of day. It started out great through because Bob gave all the interns free 4GB flash drives to use during our internships or for our own purposes. We also made a plan so that all the interns could eat lunch together at global village. Then Elaine and I went to Dr. Hornak's office and learned more fundamentals of MRI. Even though he only went over information for an hour and a half, I found it incredibly helpful. Yesterday was just taking in so much information, but today I was able to start making some connections and was able to begin to understand the material. Dr. Hornak has taught us basic principles of MRI, and now I am beginning to see the cross references to the computer program that is connected to the NMR machine. I'm learning from the science that Dr. Hornak has taught to use the program to get the image, ways to make the process faster, how to get it to 2D, and ways to improve resolution.
            Around 10:30, Dr. Hornak left because he was not feeling well. So he asked Elaine and I to continue to read his online book on the basics of MRI and also take the online RIT lab safety course so that we can work with lab equipment. My password kept being rejected at the safety course log-in, and Joe Pow directed me to the ITS Helpdesk to resolve the problem. They had to send the issue on to someone else who could fix the problem, and they were going to update me through emails. When I checked my email, they had confused my identity with one of the other interns, so I had to get that corrected. After many more emails, a phone call, and another trip down to the service desk, Kristi was able to fix my problem. Throughout the entire process, everyone who helped me was incredibly gracious and pleasant.
          Elaine and I are continuing to brainstorm possible samples to image with the NMR machine. I had fun today because I got to catch up on anything I needed to do and do it.

Thursday, July 7, 2011

Day 2

        Today, Elaine and I learned tons about the basics of MRI from Dr. Hornak. We covered areas including math principles used in MRI such as integrals, differentials, and convolution. We also spent some time on the important physics concepts, most notably, spin physics. Having taken previous physics courses, it was interesting combining past knowledge with the specifics of MRI. After a few hours of learning about the science of MRI, we went down to the lab.
         The NMR machine got refilled with liquid nitrogen while we were there. The nitrogen was pumped through plastic tubes into the machine. It was a lot of fun to watch because the tubes had a layer of frost within a matter of minutes. While we were in the lab, Dr. Hornak gave us a tutorial on how to insert a sample into the NMR machine and use the program to image a thin slice of it as well as to find the frequencies of the compounds within the sample. These frequencies could then be converted into pixel intensity and thus you get an image. We also learned how to adjust the program to have an optimal signal reading from the machine. Elaine and I then got to do it on our own and we imaged water and capulary tubes in water. Now we are currently brainstorming possible substances to put in the tube that would display an interesting image slice. The catch is that it has to be small enough to fit into a 4.5mm diameter tube but large enough for the NMR machine to display a detailed image. It's been very interesting so far and I feel like I'm learning so much. Looking forward to tomorrow...
Capulary tubes in water


Wednesday, July 6, 2011

First Day!

        My name is Sarah and I am just finishing up my first day on the job. Today was a lot more fun than I had imagined. We started the day with a general staff meeting and got the business parts of this job all set up. Our task for the morning was to go throughout campus and find designated objects, also know as a scavenger hunt. We were split in three groups and we were competing against each other for imaging science t-shirts. I am sad to say that our team placed second so no free shirt for me. 
NMR tube
NMR spectrometer
        This afternoon I talked with Dr. Hornak about the plan for the summer. What I know so far is that I will be working with Elaine and viewing images of objects less than 4.5 mm in diameter with the new NMR machine. Together we are supposed to find substances in which the NMR will show a "pretty picture." To help us with this Elaine and I have to read up on the basic principles of MRI. Today was a lot of fun and I'm looking forward to tomorrow.