23/1/31: Last Friday, Jan. 27, I had a meeting with Luca Guiga from St Monica’s and now feel so much better about my coding project. I have an assignment from him to complete before I go back there next Friday. I was sad to know the coding I’ve done for months was basically nothing, but I am now happy to learn and actually understand what I am doing.

23/1/4: Today is my first WISRD class back from break. My plan for this week is to set an agenda for this whole semester to make sure I am prepared and organized. I also want to develop my coding and reach out to coding people to help me, because I need help!!! Lastly, I want to reach out to my PI Max and the rest of my group to touch base.

22/11/17: I am adding on to my hour of code video script today for later after school when Ivy and I make our video. Here is the link for that https://docs.google.com/document/d/1Rm3AYwstMAMWMI3mVDyjsgrHmAjkY8t_Wbn95U7PODQ/edit

22/11/8: I haven’t updated this journal in exactly two months!! I have been busy with WISRD, but also with other classes, so it has been a lot. Today I am going to work on my inquirer article because it is due next week. I haven’t been very motivated in WISRD this year, but I really want to be, it’s tough.

22/9/8: This week in WISRD has been hard for me. My coding process has not been the smoothest but I am determine to figure it all out. I have most of my workflow figured out, but one section of it will not run through. I am going to continue working on this hopefully this weekend or near that time and FINALLY work it out.

22/8/30: Last week in WISRD I didn’t make much progress in my coding but this week I am dedicated to run a workflow so I don’t fall behind this semester on my goals. I am going to do even more research because maybe new data for PlantCV has been collected since I’ve looked in the past. There hasn’t been much out there about how to continue past the point I’m at.

22/8/24: Today is my third day of WISRD for my junior year. The first day Megan give us info about the year. The second day I ran the BrainWaves lab with Canada Cunningham. We sadly didn’t have success with the headset though. Today I am setting a goal for myself to make progress on my PlantCV coding or writing piece.


22/5/16: I finished my vitae today and am I waiting for comments from Joe to implement them before my job performance review on Friday at 1:15. I am now working on starting a PlantCV white paper but I still haven’t gotten all I wanted to get done on PlantCV so I need to work on that at home and write the paper here. I don’t know why the program I use doesn’t work on any of the wifi’s here but it gives me a chance to be detailed about my coding process. I want to learn why this isn’t working.

22/5/10: A couple days ago I encountered an issue with opening a PlantCv environment in anaconda with Jupyter Notebook. I emailed Lucas Guiga about this but unfortunately I did not receive a response to this email. After this I then asked Joe for help with this issue. He was attempting to see if this issue was occurring because of a problem with my computer but much of what he did wasn’t working. When he was working to help I started researching again to found a loophole. Eventually I found a way to create a workflow from scratch in Jupyter Notebook. While this wasn’t the exact same thing as what was included in Lucas’s research paper, I think the segmenting will work just as well. I’m hoping so. Today, the 10th, my computer isn’t letting me onto the Jupyter Notebook link. It seems saying reload and doesn’t end up working. I tried using all the wifi’s including my hotspot but nothing worked. Because of this I think I will continuing adding to the workflow at home.

22/4/26: Last night was the spring poster session. This time around I made my own poster showing the measurement process for the hydroponics group. I think the presentations went very well. I answered the questions that everyone asked and after I talked to each person they said it was great and they can’t wait to see our group in the future. In addition Dr. Joanie Banks Hunt said she was proud of me after I presented to her. This made me especially happy because she has became a role model to me in the short amount of time she’s been here. Overall I think our group did much better this time than last time.

22/4/11(pt 2): I just now learned that the last group did not focus on measuring the height, length, or width of the plants, instead they measured the humidity, temperature, and physical observations, which I had not assumed. So far I haven’t found anything that mentions taking the mass of the plants, but the results the last group got included grams(used in mass measurements). I am actively trying to find this information. I am disappointed that all the work I’ve been doing for a few weeks is unnecessary because of a couple of reasons. The work I did making the plan for the seminar is unnecessary because the group won’t be doing the seminar. In addition the work I did for the leaf measurements two weeks ago is unnecessary now because our lab has been off and the data is gone. But I will use this as a learning opportunity for the future and from now on all the work I do will be important to the process of our lab. This day after a break I learned a lot about what should have happened with our lab.

22/4/11: Today I noticed that the lettuce plant furthest to the left on the first row is dead. The leaves and the roots. On break the water wasn’t flowing to the plants, the system was turned off so it makes sense that this plant died. I learned now that before a break it is very VERY important to figure out a plan with the measurement of the plants. Harvesting them could have been an option but we weren’t organized enough to determine the plan.

22/3/22: Today I learned about a new process of measuring that involves math that I have done in past classes. The process is….

  1. Printing out a picture of a plant
  2. Cutting out the leaf
  3. Cutting out a square and finding the area
  4. Taking the mass of both of the papers
  5. Finding the ratio between the mass of the square and the mass of the leaf
  6. From that getting the area of the leaf
  7. Making a graph so then whenever I have the mass I can find the area and vice versa.
  8. I can also find the ratio of mass to area

22/3/15: I learned today the correct way to make an agenda, the correct formatting. I finished the general version of the agenda, but I don’t know all the specifics that I should add yet. I will continue to work on the agenda based on the youtube webinar video and I’ll add the rest later.

22/3/14: I just got back from my two week recovery because of my knee surgery. I feel like I’ve missed a lot within my project. The plants have grown a good amount while I’ve been gone. For the measurements of our plants it would be hard for me to do it on crutches, so someone else in my group has to start the process and I can take the photos everyday for it. Joe also had an idea to set up a seminar with people from St. Jude’s school about PlantCV. I am going to start the agenda for that, and base it on seminar’s PlantCV contributors have already done. The doc for this agenda can be found here.

22/2/8: Yesterday I created a flow chart for my measurement procedure, and today I finished it. It includes all the steps I went through. This will be a helpful reference for the next time I have to complete measurements. Hopefully the next time I complete measurements I can do it via PlantCV, but I’m not sure if I’ll get there yet. I’m learning more about it everyday though. I’ve never done a flow chart before, I have seen them, but this is my first time learning how to do one.

Here is a photo of my flow chart based off of a formatted website. The square shapes represents the steps in my procedure while the triangle shows ideas that I have, basically the mental aspect to it.

22/2/4: I measured the height of the roots today. It was very challenging to do because the lettuce is mostly dead. Touching it at all made pieces fall off. The number of leaves could not be measured since some have fallen off of the plants. The same could be said about the roots, but I still chose to measure them since they are an important part of our data.

22/2/3: Today I learned about my research field a little bit. My favorite fact from my notes was that the University’s Hounsfield Facility uses a root phenotyping installation based on X-ray computed tomography. I thought this was interesting because I had an MRI done for my knee before. This system is similar to one for a MRI.

Example of Machine

22/1/31: Last week I took photos of the plants to measure them. This weekend I finished the measurements on google slides. From an email Joe sent I learned what the last Hydroponics group did for their measurements.

Table of Measurements for All Three Plants
Example of the measuring process

22/1/18: I just learned how to make a workflow that creates the changes in an image. I used a youtube tutorial to help me with this, and I also used the sample workflow available to gauge how I can fill mine out. I am still a little bit stuck on how I can alter the workflow to fit the sample image I have. But this week my goal is to code over my sample photo with no mistakes.

Example workflow

22/1/11: Today I watched a workshop video on youtube about PlantCV. I learned about thresholding which for example could take a RGB image and change it into a LAB image, ultimately changing the colors in the image.

21/12/16: I have been watching videos to download and start working on PlantCV. Since my article and research are done, my main focus is now PlanCV.

21/11/18: Today I encountered an issue trying to download plantcv with anaconda. I looked at the aricles about the download and learned that I could also install plantcv with pip. With this new discovery I will have plantcv downloaded and start coding either today or in this week.

21/11/10: I finished my article for the Inquirer about plant mutations but it ended up being a little short. When editing it for my second draft I will add more information to increase the length a little bit.

11/9/21: WISRD had a successful poster session last night. I talked to lots of people about our project and shared how the hydroponics lab is looking into incorporating PlantCV into our research

21/10/26: Today I researched the nutrients needed in our water that the previous hydroponics group used. I didn’t have luck in this research so I had to email to find out. I emailed Luis Perez, a senior in WISRD, to ask him about his sister, Ximena Perez’s pervious work in WISRD. After hearing no response our group found our own nutrient solution to incorporate in our lab. Today I also learned about a new coding program that would immensely help our group measure our plants. The software is called PlantCV. Upon learning about PlantCV I was very interested, so today I also committed to being the head coder in the PlantCV software for our group.

PlantCV is an open-source image analysis software package targeted for plant phenotyping.

21/10/21: After a long time of work, I finished my vitae today. I think I could maybe add a little more detail but right now I am going to continue writing my article for the Inquirer. I am thinking about adding information about GMO into my article to expand on the modern day advancements.

Here is an example of a GMO tomato compared to a regular one

21/10/5:Today the whole Hydroponics group come in and took a photo in front of the rig. This photo will be uploaded to our project page and sent to Joe

21/10/5: I finished my pitch for an article in the Inquirer newspaper. The topic of my article is mutations in plants and how they affect the agricultural system. After researching this topic for the hydroponics project I was very interested and wanted to learn more about it. So making it the subject of my article allows me to do so.

21/9/27: I tweeted for the second time on the WISRD twitter to announce lights being added to our system. The tweet can be found here.

21/9/14: I tweeted for the first time on the WISRD twitter to announce the lab being cleaned up and ready to get set up. I included a fun fact from my research to add an exciting aspect to the tweet. The tweet can be found here.

21/9/13: Today we ran the repaired lab to see if there were any mistakes or anything we have to change. I helped to organize the station and set up the lab. I filled the lab up with distilled water, cleaned up the area, and studied the lab to really determine what’s working and what isn’t. I decided to look over past procedures because I was a little confused about the whole process.

21/9/1: I emailed Max A.S. (24′) and said I am interested in hydroponics, now I am now officially in the Hydroponic group. We now have a document with our assigned jobs. I am going to start researching lettuce genetics and mutations.

21/8/24: Today was my first day at WISRD, I am thinking about joining the Hydroponic group, because I am interested in life science, so I am looking over their page and articles.