Blog Posts

Prototyping Progress

Published:November 5th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

With absolutely nothing at all happening in the rest of the country, team Macro Mice spent the week hard at work on both the digital and physical fronts of the project. For the behavioral unit, Daniel has made great progress in finalizing the designs for the first iteration of the prototype. After touching base with the IPPD lab manager, the team is now ready to begin manufacturing components and has begun sending 3D printing requests to the lab. Beginning next week, we will begin assembling the first full iteration of the project! 

On the software side of the project, we’ve run into a problem where the course’s main source of version control Gitlab, is continuously giving us problems with logging in. We have temporarily created a GitHub repository and plan to work there for the time being, until GitLab stops giving us issues. We plan on integrating both cameras and infrared sensors into our design, and we will continue to refine our image processing software accordingly with these new additions. We will then begin testing our software with the images provided by our liaison.  

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Prototyping Begins

Published:October 29th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

This week as part of the selfie system team, Derek has been having trouble with the processor speed of his Raspberry Pi. After following all the instructions for installing OpenCV, he used “make” and the Raspberry Pi has been building for over 24 hours now. He hopes to finally finish installing everything by tonight so that he can begin contributing code and doing testing. In addition to this, Aaliyah used this tutorial to start an image processing program. However, that solves the problem in a 2D way, and the mice live in a 3D world. We must begin thinking about a different solution. The group has also recently purchased infrared sensors that will serve as the trigger our software to begin executing (taking photos of the mouse and analyzing the diameter of the wound in the picture taken). 

While the selfie system team has been hard at work, Daniel has been designing the 3D models of the physical enclosure. This process began with an analysis of previously measured size data of the mice. Once averages and a standard deviation was taken for seven different measurements, the necessary sizes of each component were determined. Using this as a starting point, the individual concepts highlighted in the PDR are now being brought one step closer to realization through CAD modeling in Solidworks. Daniel hopes to begin manufacturing these components next week! 

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PDR Presentation

Published:October 23rd, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

On October 22nd, we met with members of the Acomys Research Consortium and presented our Preliminary Design Review (PDR) to them. We received a lot of valuable feedback from the members and got to introduce ourselves to some members of the ARC we had not met before. With the help of the ARC’s recommendations, we have made some adjustments to our project design and hope to get started now that all hardware components have arrived! 

Screenshots of our meeting courtesy of Dr. Edward Latorre.

Going into next week, we will be utilizing the feedback and advice provided to begin progress on our first prototype! With specific goals and objectives each week, the following month is all about bringing all the work until this point together, and start working on the actual coding, wiring, and 3D modeling. We could not be more excited to take this next step in our project and look forward to getting something working by the end of the year. 

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PDR Preparations and Prototype Beginnings

Published:October 18th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

By far the biggest activity this week was our Preliminary Design Review (PDR) presentation peer-review. For those who are unfamiliar, the PDR presentation, and by extension the PDR report, is the first chance where each individual IPPD team gets a chance to show their current project plans to their sponsor company outside of their point-of-contact liaison. This presentation is next week for us and the peer review gives us a chance to refine it before the big day. While we ran into some technical issues, we bounced back and the feedback we received from our peers was extremely helpful. We have taken these comments into consideration and we feel confident for our PDR presentation next week. Now to tackle that pesky report. 

In other news, Derek is learning remote this semester, and there has been a delay in receiving parts as a result. All the Raspberry Pis have been received and all the cameras should be in by next week as well. Hopefully with IPPD assignments slowing down and all parts being in our possession, we can begin coding up some tests for the image processing software and start printing some basic housing unit components to test on with the mice.  

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A Small Update

Published:October 8th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

Team Macro Mice has been hard at work on the beginning stages of our project. After obtaining 32gb micro SD cards, we finally had enough space to download and install OpenCV on our raspberry pi. We followed the tutorials that were linked in our last blog post. We hope to begin coding and testing different cameras when they arrive. A word of warning to those planning on installing OpenCv on a raspberry pi: it will take about 6 hours to do so. You can speed up the installation process, but run the risk overheating the system. 

In addition to the aforementioned progress made on the computing front, we were able to take strides in the physical design of the prototype as well this week. From discussions with Dr. Varholick, in person evaluation of mouse behavior, and measurements made on mouse cadavers, the concepts for physical components has begun to take shape. Sketches highlighting multiple concepts for each core component of the prototype were produced and approved. We are ending this week with 3D CAD models of the designs being prepared for completion in the following week.  

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Hardware Hurdles and Meeting Mice

Published:October 1st, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

Earlier this week, we attempted to use Open CV on a Raspberry Pi. Some tutorials that were helpful were this one from Open CV and this one from Py Image Search. However, we only had an 8gb micro SD card for the pi and after updating the Raspberry Pi OS (Raspbian), there wasn’t enough space to download and build Open CV. We have ordered some 32gb micro SD cards and plan to try again once they arrive. 

Derek is working from home in South Florida and is still waiting on approval from the lab so equipment can be sent to him. He needs materials so he can begin coding and recognize the hardware limitations and software compatibility.  

On the physical side of Spiny Mouse Selfie, Daniel met with Dr. Varholick and our spiny stakeholders to better understand their behavior, the enclosure’s design requirements, and our liaison’s expectations for the project. After this meeting Daniel is rearing and ready to go to work on creating conceptual designs and models for the mechanical components of the project. 

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First Steps

Published:September 24th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

This week Team Macro Mice laid the foundation for the project at hand. With microcontrollers and cameras beginning to be ordered, the team will begin working on developing the electronic and software aspects of the project! We hope to start working with Open CV to create the image processing software. Additionally, the team now has access to a functioning 3D printer, which will be used to create the first prototypes of the project. With all this coming together, the team is excited to move forward with the first steps of conceptual design! 

In addition to the work done on the design front, the team has also devoted resources towards developing and refining as clear a roadmap possible for the future of the Spiny Mouse Selfie. Exploring potential risks, deadlines, stakeholders, and potential opportunities of the project has allowed the team to prepare for anything the world can throw at us. 

The Spiny Mouse Selfie

Published:September 18th, 2020
Category:Aaliyah Richlen, Daniel Levy, Derek Mackey

The spiny mouse is the only known mammal capable of regenerating tissue to the skin, ear, skeletal muscle, kidney, spinal cord, heart, and brain. The unique regenerative properties of the spiny mouse have made it popular in research. However, when observing the mouse and how fast its tissue has healed, researchers are forced to either a) hold the mouse gently in a towel or b) administer isoflurane anesthesia to the mouse. Holding the mouse can be an issue because the skin of the spiny mouse is 8 times more delicate than human skin and is prone to tearing easily. This method also only allows observations to the head area, since holding the mouse can be difficult. Administrating isoflurane anesthesia has been shown to cause distress to other mammals, which may delay the healing process and give inaccurate results. Because of this, the Macro Mice team is partnering with Dr. Malcolm Maden and Dr. Justin Varholick in the UF Department of Biology to create a housing unit that will take a picture of the healing hole of the spiny mouse and measure that hole as the mouse eats. This system, the Spiny Mouse Selfie, will hopefully give other researchers a cheap and easy way to study the regenerative properties of the spiny mouse. 

Image of the Spiny Mouse courtesy of: https://upload.wikimedia.org/wikipedia/commons/d/d8/Common_spiny_mouse_cropped.jpg

Where we are now: We have clarified more specifications about the hardware we are going to use to capture this data, but we still need to do more research before we reach a definite conclusion on what parts we are going to use. We are currently looking into PixyCams, the IMX2019, and Raspberry Pis. We are also looking into the Raspberry Pi’s compatibility with OpenCV, a popular image processing library that we could use.  

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