Charles Hockaday, Jr.: The Open Microscopy Environment (OMERO) for Digital Marine Organism Imaging

About me: I am Charles Hockaday, Jr. I am a junior at Elizabeth City State University studying Computer Science.

Project: The Open Microscopy Environment (OMERO) for Digital Marine Organism Imaging

Mentor: Andrew Mount

Weekly Report

Week 1: As of the first week at Clemson for my research I was able to learn about how to use software known as Paraview and OMERO. Both pertaining to needing a lot of data to be used and to make 3-D images. After learning about the two I needed to install them both in order to use them and play around with it before receiving biological data and putting it in. Now I just have to configure Python with OMERO and I’ll be squared away as week one comes to an end.

Week 2: I was able to finally download OMERO and Paraview onto my PC. After that was completed I had to become accustomed to using both of the types of software and along with that be able to configure Python with OMERO. I was going to also try to connect paraview to the palmetto cluster but an update had held us back on that task so I do not know if that can be done at the moment. I received images from Vera and toyed around with it on OMERO and have been able to make some progress on using the software.

Week 3: Still have not been able to connect paraview to the palmetto cluster. This week I was able to convert the images that I received from lif to tiff format. Once that was complete I am now in the process of trying to get that stacked image into 3-D. Along with that I had to download more material onto the computer so that I’m able to use python shell in order to make the 3-D image.

Week 4: We finally decided to not add the palmetto cluster. I continued to mess around with OMERO and try to connect it to paraview by using the python shell on the software. Along with this process I am to make a power point presentation of our work so far. I will discuss the basics on how to setup the software called OMERO and how it works. Not only will I discuss OMERO but I will discuss the setup of paraview as well and how that software is used. Before I began working on the power point I tagged along with Dr. Mount and Vera to collect oysters in Georgetown so they can collect data from them for future works.

Week 5: During the middle of this week I had to give a presentation on what I had done so far for the midterm presentation. I only discussed the basic setup of OMERO and how to use it. I did the same thing when it came to paraview as well. Overall the presentation seemed to be a success. Afterwards I began to continue to work on the paper but is having problems setting up Latex on my laptop so that I can work from home. I’m still in the process of trying to figure out how to transfer images and get everything to work smoothly and the process is taking its time but everything will get done as soon as possible.

Week 6: After doing more research into OMERO we were able to figure out how to visualize an image in Paraview. It was a simple process that we had to go through for both ImageJ and Paraview. The process of importing the data to ImageJ then along with that securing the important information such as the height, width, and the depth of the image. With this information a user would need it to input into Paraview in order to accurately get an image to display on the screen. This process started to not take as long once we realized everything that was going on within the ImageJ and Paraview interfaces.

Week 7: As this week approached I proceeded to working on the final report of this entire project. Along with the paper I have been working on a presentation for the final as well. With the final presentation I took the power point from the midterm and added some slides to that after receiving more information and understanding of what I was doing. With a paper and a final presentation I also had to make a poster. On the poster I was just going to add the abstract, introduction, conclusion, future works, and also images for people to view of the data that had been collected and ten visualized.

Week 8: During this last week of the summer REU I was able to finish my final power point presentation also finish the paper and poster. For the past 8 weeks not only was I able to finish everything that was assigned but I was able to learn things that I probably would have never attempted to learn while in school. I am glad to have received the opportunity to enjoy this experience and work with the people that were with me from the beginning of this program. For future occasions I wouldn’t mind experiencing an internship like this again. There is always a chance to learn something new when it comes to summer research.

Final Report