Wednesday, July 31, 2013

Return of the Annoying Technology

July 31
Day 18

Hello, did you miss me? I was out yesterday so I didn't do a blog. But I'm back.
This morning was reasonably quiet, I spent most of it making image cubes for a new manuscript that I am working on. Those don't take long, but they do get tedious. After I calibrated the cubes I am going to take certain bands and, using  common principal and independent components, turn the images into a Polynomial Texture Map. It's confusing, and even my adviser hasn't used this method of imaging before, so it is going to take a lot of trial and error to find the right system. Hopefully it doesn't turn out to be too confusing once I can actually get started. Unfortunately I  have not been able to start making the PTMs yet because the computer has decided to go on strike and not accept any disk drives when I plug them in. That and confusion over which disk drive that data that I need is one has caused me to lose a large chunk of the afternoon. By tomorrow (I hope) I will have the files so that I can get started working. Why, technology, do you feel the need to be so troublesome? Why?

Here's hoping tomorrow is a better day, and I can get more imaging done. But that really all depends on my computer.


Monday, July 29, 2013

Clean Room Conclusion and New Projects

July 29
Day 16

Hello. we finished building the clean room today It was a lot of fun and a great break from working on manuscripts endlessly. I really miss robotics; building things and working on a team. Hopefully the clean room will be wired and ready for use soon and that research can get started in it.

Today Roger came back with new data for us from LA. I get to work on Polynomial Texture Mapping images of two manuscripts in Latin and possibly a Roman mummy portrait and a Roman statute. The Latin manuscripts are exciting because I took Latin in school and I am able to translate the visible parts. Its really cool to be able to use something that you learned in school in the real world. I am very excited about this because it I a new type of processing and I get to do something different than what I have been doing for the last 3 weeks. I am hopeful that these images will turn out well. If you are interested look up Polynomial Texture Mapping, its really cool. It involves taking pictures of an object with the light coming from different angles then compiling them all together and essentially creating a 3D image.

July 26
Day 15

Hi. Today was a very short day for me. I left after the picnic so I only worked during the morning. I managed to get a few files done, but my computer was running really slow. Apparently it couldn't wait for the weekend either. The picnic was fun. The weather was nice and Bethany brought her adorable dog. Monday will be fun, as we get to finish the clean room. Really looking forward to that.


Thursday, July 25, 2013

July 25
Day 14

Hi. Today was very busy. This morning we peer reviewed our abstracts for our final presentations. Mine was okay, I just have to shorten the title and add some more about exactly what type of imaging I am doing. All of the other interns' presentations sound really cool and there is a wide range of what people are doing. Some are working with more hands-on building and testing and some are writing code. I think the biggest issue for all of us will be trying to remember what all of the acronyms stand for.

I finished the skipped over leaves and got to move on to a whole new batch today. I am making progress which I am happy about, though the endless stream of leaves and manuscripts is more than a little daunting.

This afternoon there was a talk on supernovae and using 3D models in astrophysics. I found it very interesting, even though I know very little about astrophysics. The abilities of super computers is amazing and allows researchers and scientists to do so much that they could not have done even 20 years ago.


Writing an Abstract

July 24
Day 13

Hi. Today our first Milestone was due. This milestone consisted of the title of our final presentation and an abstract summing up our presentation subject. I am going to present the research that I have done on the differences in the processes of imaging the leaves based on the side of the parchment and the damage done to the leaf. Each leaf has to be processed separately and you have to look at each band separately to find the best combination. This takes a long time and would be difficult to automate. The other part of my presentation will be on how the "outside world" impacts research. The manuscripts that I  am working on now are from Sinai, Egypt and because of the current revolution it would be difficult for researchers to go there to look at the manuscripts. I find that really interesting and while it isn't exactly imaging science, it does apply to the research that we are doing. Writing the abstract itself wasn't that difficult, as it was in the same form as the projects I had to do for an online program I did with NASA through the Women in STEM High School Aerospace Scholars program.

I continued to work on the leaves from the manuscript I have been working on from the beginning. Now I'm just going back and doing the leaves that were skipped over before, and there aren't that many, so that's good.

Today's video was about Patent laws and the changes that came in March of 2013. As someone who wants to be an engineer and wants to invent things this was actually interesting to me and will probably become very important.


Tuesday, July 23, 2013

Accomplishments and a Platypus

July 23
Day 12

Hello. Another exciting day at CIS, finding ancient secrets and treasure maps. Okay, so maybe not as intense as that but still a good day. I finished up the files that my adviser Roger Easton assigned me personally. Yea! Now I am gong through the rest of the files on the disk and doing ones that were skipped over before because they weren't as important to the scholars or they were difficult. Each leaf (page) is so different from any other that there is no set in stone method. You have to look at the bands (the images taken using different types of light) each time and determine which bands look best for that leaf. A lot of the time the leaves will use similar bands, but the rest of the process is specific from each leave. I'll talk more about that tomorrow. I don't want to give you all the secrets at once.

We now have an official CIS intern T shirt design! It was made by two of the other interns, Mia and Simran. Hopefully the shirts will be in soon. Let me explain the design before you get really confused. The Center for Imaging Science mascot is a platypus, because it is a mixture of lots of different animals and imaging science is a mix of many different fields.  He is surfing on a wave because its summer and that is what platypi do on their vacations (and the wave is part of the CIS official logo). Hopefully, that clears up any confusion.


(For those of you who don't know DFTBA means Don't Forget To Be Awesome)

Monday, July 22, 2013

Building a Clean Room

July 22
Day 11

Wow. Its day 11 already. That's scary.
Today I did not on the manuscripts very much, I ran a few bands of one leaf but that was it. My advisor, Roger Easton is out of town for the week so I am continuing through the leaves that he left me to do. I spent almost all of my day building a clean room. It was so cool. We literally built a room inside of a room. We had to connect all of the supports and walls and put in the plexiglass walls. It was a nice change to be able to do something other than on the computer. I am on a FIRST Robotics team, so working together with people to build things is something that I love. Robotics is the thing that I miss most about the school year during the summer, so this was a nice chance to get back to working in the fashion. It was a fun time getting to know the other interns better as we built something that will actually help in research. We didn't finish it so we will go back later in the week to install the ceiling and the rest of the walls. I'm looking forward to it.


Sunday, July 21, 2013


July 19
Day 10

Hi. Sorry this post is a few days late. I left early on Friday to take my road test and I forgot to do my blog. (I passed) Since I was only there for a few hours on Friday I don't have much to report. I continued to work on the Georgian manuscript form Saint Catherine's. At lunch we had another picnic and played more volleyball. It was a very nice relaxing day, other than the road test which was stressful.

Something very exciting did happen Thursday afternoon though. While leaving the building I met Derek Muller, the host of Veritasium. Veritasium is a science channel on Youtube, and it is one of my favorite channels. It was awesome to meet a personal hero and talk to him for a little bit. Anyone who is knowledgeable about something and shares that wisdom and their love of the subject on the internet for others to benefit from is a hero to me. I think that the future of education relies on channels like Veritasium, and others like Scishow and Crashcourse, to get people excited about learning things just for the sake of learning. I would definitely advise checking out his channel as well as other educational channels, such as Scishow, CGP Grey and minutephysics.

Thursday, July 18, 2013

Helping out

July 18
Day 9

Hi. Today I actually spent a lot of my time helping out with other people's labs. I helped to clean up the building materials for a clean room that another lab is building. There used to be a clean room in CIS but then it wasn't needed anymore and it was taken down.  All of the clean room equipment has been in storage for a few years. I have never seen so much dust. Ironic. On Monday we get to help set up the clean room, which I am really looking forward to. I think it will be really interesting to see how they build it to keep it so clean. I also got to assist with a senior project in Color Science. It was very interesting and I am glad that I could help the student with her research. The environment at RIT is one that encourages people to help out in other research, which I think is really nice.

Of course, I also did more work on the manuscript. No treasure maps so far, but I'm still hopeful.


Wednesday, July 17, 2013


July 17
Day 8

Hi. Today I continued on with my work. You know how I said that I had finished the hard ones? Nope. Some of these new leaves don't even appear to have any undertext on them. Which is very disappointing after you have spent half an hour getting all the files in order and renaming all the bands, just to find out that there is nothing visible. But today was good in that I finished my 20th leaf of the manuscript I am working one! (a leaf is one side of a page, and a manuscript is the book) So that's been fun. But hopefully I can try a different method tomorrow and get some better results.

Today all of the interns went to a presentation on giving presentations. It was all about trying to incorporate the ideas of zen into a good presentation. It will be very useful when I have to give my final presentation on historical document restoration at the end of the summer. All of the interns then played Uno, which I won, much to my own surprise.

Here's hoping that tomorrow the manuscripts stop withholding their ancient secrets from me and I can get some better results.


Tuesday, July 16, 2013

A Miracle

July 16
Day 7

Can it be? Is it possible? No problems with technology today! Finally, it seems I have stopped breaking things and can get down to the actual work I'm supposed to be doing.

I was able to fly through my work today, I am really getting better at ENVI. At this point I have memorized all of the wavelength codes for the color bands that I am working with. It can be difficult though to find the best combinations of bands for each leaf. Each band of each leaf has different results of varying usefulness, so you have to try and combine them in different was to get the most readable option. This requires a lot of time consuming experimentation and disappointment. But eventually you find one that is passable and then fix it up in Gimp.

Not much else going on, just continuing to work through the St Catherine's manuscripts and playing Apples to Apples with the other interns during lunch. Overall, a good day.

Here's hoping my luck with computers holds.


Monday, July 15, 2013

Gaining Speed

July 15
Day 6

Hi. Today I actually managed to get a lot of images done. I made it through 5 and a half leaves, which I think is a lot for one day, at least compared to what I have been doing. And excusing the brief moment where my computer lost the internet, not technology issues either. The leaves that I am working on now are easier than the ones that I did before. This is partially because I am getting better at the software and partially because they are not the top priority files, which are apparently the hardest. Overall a productive day.

I really wish I could understand what these manuscripts say. I want to know if the image I'm working on is a letter or a speech or a shopping list. It really doesn't matter, but I think it would be really interesting to know.

Sorry for the short post today, but when nothing goes wrong with the computer I basically just use the software. Not very exciting, but interesting all the same.


Friday, July 12, 2013

More Computer Issues and a Picnic

July 12
Day 5

Hi. Today was another day of battling with technology. My computer decided to not recognize any disk drives, so I couldn't get any more data. Eventually I was able to get back to work but the computer issues are really slowing me down. I managed to get through the rest of the high priority leaves that I was supposed to do. These are the most difficult ones, so now I get to enjoy some easier ones. I found some really cool symbols on one of the leaves, much larger than any of the other characters. I wonder what the are. Unfortunately, I don't read Old Georgian so I have no idea.

I also discovered that when using this software and trying to make the undertext more visible the parchment can look really cool. When  trying to reveal the undertext you put different bands in to the red, green, and blue parts if the image. This makes  the text change colors, and any dirt or other stuff on the page also change. By the end the parchment kind of looks like dragon skin or a galaxy, lots of colors and swirls and spots. I'm really surprised that no one has used this to make art.

The highlight of the day was having lunch outside and playing volleyball with the other interns. Every Friday a grill is set up outside and anyone in the building can go cook and picnic outside. It was a beautiful day and we had a lot of fun.

Overall, my first week was great and I'm looking forward to the rest of the summer.


Thursday, July 11, 2013



Hi everyone! This my official introduction. Hi, I am Mary Emma. I am a rising senior at Our Lady of Mercy High School. I am interested in science, robotics, reading, and camping. I am a huge nerd, and proud of it. I love Harry Potter, Sherlock, and Star Wars. You get the idea. This summer I am an high school intern at the Center for Imaging Science at the Rochester Institute of Technology. I am one of the Historical Document Restoration interns. There are 13 other inters all in different labs. We are each required to keep a daily blog to keep the world updated about our research. You can find the links to all of these blogs here:

Thanks so much for reading my blog, and if you have any questions leave a comment. But be nice. Thanks.


Computer Troubles

July 11
Day 4

Hi! Welcome to day four of my internship. Today my computer decided that it really didn't want to do anything. Its memory was very full, which I didn't know. This caused it to become incredibly slow. Apparently the Force does not work on computers. I spent an hour waiting for a few files to open. So now I've got to transfer all of my files to a disk drive. So over all, I didn't really get to do much imaging today. Sigh, technology. Why must you be so temperamental?

I did manage to get some new leaves of the manuscript done today, but most of my time was spent going back and tweaking manuscripts that I did before. I was trying to make them more readable, which is very difficult. The fact that the parchment and the undertext are so close in color is a really big issue. When ever I adjust the hue angle or change the contrast or anything they change together, so it is still really hard to read.

Hopefully tomorrow my computer will cooperate and I'll be able to get more done.

One good thing that happened today was we talked about when the lab imaged the Archimedes Palimpsest. My adviser, Roger Easton worked on the manuscript and its really interesting to hear about it. He has a copy of the book The Archimedes Codex by Reviel Netz and William Noel. Its really interesting. I've been reading it as my computer loads, and so far its really good. I would definitely advise reading it if you are interested in this subject.

I hope to have more to tell you tomorrow.

Wednesday, July 10, 2013

Figuring things out, hunting for treasure and eating pizza

July 10
Day 3

Hello, again. Thanks for checking out my blog. I will do my best to keep you informed and entertained with the goings on of a day in the life of a Historical Documents Restoration intern. Today I continued to work on the manuscripts from Georgia (the country, not  the state). I have no idea what they say but for the sake of all the work I put into making them easier to read I hope they aren't someone's shopping list or something. I am actually becoming faster using the ENVI software. I think it's one of those things where you do it a couple times and then the system just becomes ingrained in your head. I got through a whole two manuscripts so far today. The contrast between the undertext and the parchment is my main problem right now. Because the undertext is faint it is so close to the color of the parchment that changing the hue doesn't really help make it readable. I'm using Gimp to do all of the hue angle changes and contrast changes, which is difficult as I am used to using Photoshop. But by the end of the summer, I'll be able to use Gimp really well. Hopefully.
      The one thing about this research is it is kind of boring. Most of it is monotonous entering of numbers into the software and waiting for my computer to load. But seeing the undertext suddenly appear on the screen and knowing that I am the first person to see this writing in thousands of years is just amazing. I think its really cool that I am seeing the ink that someone thousands of years ago, halfway across the world used to write down their thoughts or a prayer or a recipe or whatever. Also, knowing that maybe these words that I just made readable could hold some sort of valuable information. Maybe I'll find a pirate's treasure map or a map to the Lonely Mountain. I am currently taking applications for a treasure hunting crew if I do happen to find such a document.
    Every week the Center for Imaging Science has a movie showing around lunch time on Wednesday. They show a couple of TED talks, which I love. I think it is a brilliant idea to provide the public with free access to experts like the TED talks do. If you haven't seen one check them out. There is also pizza, popcorn and soda provided at these movies, which was a nice plus. Yea, pizza. But seriously, TED talks, check them out!

Tuesday, July 9, 2013

First Day of Actual Work

July 9
Day 2

Hello. Today I actually got to start working on some manuscripts today. After the morning meeting of the high council of interns we split off into our labs. Under the guidance of Liz I learned more about using ENVI. The work is tedious, mostly entering a lot of data into different boxes. But once you've done that and the image appears, the fun starts. I have to look at the manuscript and see if I can find any undertext. The way that is historical document imaging works is that using different lights and colors, you are able to see the undertext. The undertext is writing that was on the manuscript at one point, but was scraped off and new stuff was written on top. This happened mostly because the materials to make manuscripts was so expensive.    So when a scribe or monk wanted to write something, they would scrape the existing ink off of the manuscript and write whatever they wanted on the newly clean material. While this was eco-friendly (and goat friendly, since the material was often goat skin) This means that using different techniques we can see what was written originally, which can provide valuable information for scholars.
         Once I got my own computer I started working on a Georgian manuscript. It was kind of confusing figuring out where all the different things go and what order to go in, but once I got the hang of it it wasn't too hard. I even found some undertext! I'm very excited and hope I can enhance the image so I can see more.

First Day of RIT CIS Internship

July 8
Day 1

Today was the first day of my much anticipated summer internship at RIT CIS. It was very interesting and I had a lot of fun. We started out the day with a meeting getting to know everyone's names and what lb they would be working in. I m working in the Historical Document Restoration lab, which I am really looking forward to. After introductions and some reading through the intern manual we received a challenge for the day. We were split into teams and were given a packet with lots of random pictures from around campus in it. Our challenge was to find as many of the items as we could and make a documentary about it. It was so much fun to run around the college getting help from students and faculty members as we tried to find the most items. After each team created its video we all watched them while being judged by a panel of highly esteemed judges. Though my team (the Green Gophers) did not achieve victory, we got to know each other really well and hopefully now know the campus well enough not to get lost.
      After lunch we split into our lab groups. Also working with me in the Historical Document Restoration lab is Calvin, a high school intern like me, as well as too undergraduates, Liz and Christian. We all work with Roger Easton, who is an expert on this topic. We went over ow to use the software, ENVI, which we would use to image the documents. There are so many cool documents, and the lab has worked on some very interesting manuscripts, from Shakespeare to the Archimedes Palimpsest . I am very excited to learn how to work with this software and help to give more information to scholars who are studying the manuscripts. Hopefully tomorrow I will have my own computer so that I can start working.