Collected Thoughts

A cathartic place for my thoughts.

The Thankfulness Anthology

I write to my mother daily, to tell her one thing I'm thankful for. 

Firstly, let me extend my gratitude to you, mother, for suggesting this idea and always sending me a message in response. In a way, I feel like it hasn’t only just made me seek out specific things for which I am grateful, but it also brought us closer together. I think this was a great idea, and I very much want to continue onto the future. Below, I have collected each of my thankful points, from 12th/December/2016, to the 24th/December/2016, to reflect and extended each of them, perhaps gaining more value from the act of being thankful. 

Thank you madre, I love you.

 

12/December: Avocados

Original message; “Today I’m thankful for Avocados. I’m thankful not only for their nutrition, but the memories I attach to growing up in the fields across the canyon. It’s a beautiful thought."

I’m quite thankful for where I grew up, and the environment in which I was raised. I reflect on some of my early memories, running around down in the back yard, past the canyon. Through the (what seemed like) thousands of trees, and millions of very stomp-able leaves, to open areas where we could look down across the San Pasqual valley, I feel fortunate to grow up where I did. In my daily life, I can’t help but associate the simple avocado with that time, and those memories. It’s something that makes me smile internally as the thought comes by, and I recognize it. Sometimes I wonder, and hope, you do the same of tomatoes, and your childhood. 

 

13/December: Computer

Original message; “Today, I’m thankful for my computer. It’s been able to make my life so much easier, I’ve been on it all day!”

I wrote this message on a day where all I did, for maybe 10 hours, was work on the computer. We had a big proposal deadline approaching, and as such, my professor dumped it all on me. I had to make complex budget tables, balancing huge numbers of components, each with price tags that would make even Sandy and Bart’s eyes widen. I compiled every part I’d need to build the proposed system, and distributed the allocated funds across three years, to appropriately spread it in accordance with the developmental timeline for adequate completion of the proposal. The first year, we are buying a laser; it costs $213,000. I think that’s a bit, crazy. I had to write thousands of words regarding the scientific merit and value of what we are proposing - I did it all, on this here device. The thankfulness I have for my computer came from that process. The writing, the tuning of the numbers, the calculation of how much tax would be collected, it was all so easy with my laptop. It seemed the obvious thing to be thankful for, for that day.

 

14/December: Ears

Original message; “Today I’m thankful for my ears. They let me hear many beautiful things, like my favorite songs, the sound of people I care about laughing. It’s somehow the most direct connection to the world, for me. Sight is really important too, but I think there is a real feeling and emotion in sound that I really enjoy and am thankful for."

On this day, I had decided to bring my nice headphones from home, to the university. They spent most of their time previously at my office at home, which I seem to hardly use these days. Seeing as I was working pretty heavily on my computer at the time, I wanted some sweet tunes to enjoy. I pulled up soundcloud on my computer, and searched for “XXYYXX” an obscure, too-cool-for-you music producer from LA. His music is underground, hard to find, hipster as hell, and totally excellent. I played his remix of one of my favorite songs “Snow in Newark” by Ryan Hemsworth, and immediately after hearing 1:47, was very thankful for my ears. There’s a lot of emotion in music, and the emotional connection I have to that song somehow was amplified by XXYYXX’s swelling, almost cinematic production. The more I thought about it, the more I started thinking about my favorite sounds. People. Music. The Environment. Sound is powerful, and really subtle. A lot less direct than sight, but somehow more connective for me.

Read More

The Auto-Focusing Microscope

I've built a lot of microscopes, and I quite enjoy doing so. When my EE209AS course presented the assignment to build a robotic system, my mind naturally gravitated in this direction, not only because of its familiarity and interest, but because of its necessity. 

--

Abstract:

We developed a sheet-illumination-specific autofocusing system, which is able to iteratively position a detection objective lens onto an orthogonal Gaussian laser beam. Sheet Illumination microscopy has made a large impact on the microscopy community recently due to its many advantages. Increased photonic efficiency allows for lower power light sources, which in turn reduce phototoxic damage to biological samples, while providing an increased signal to noise ratio in the final images [1-5]. However, due to increased geometric complications over standard microscopy systems, fine positioning of the image plane is absolutely crucial. In order to do so, we developed a light-sheet feedback-based focusing system. This robot is capable of automatically focusing itself, to improve image resolution despite sample-specific shifts in the laser’s position. The system is built on a specifically designed testing platform, equipped with a SONY image sensor, a Raspberry PI 3, and a stepper-motor. Image processing and all system controls are handled by the Raspberry Pi. Included in this report are the basic descriptions of how this project was implemented, comprising of background knowledge prior to this design, experimental methods, and analysis of the results.

Introduction:

Sheet Illumination is a rapidly-developing field of fluorescent microscopy, which relies on the decoupling of standard illuminative and detective processes, which typically coincide in standard microscope systems. Despite many advantages of this imaging modality, geometric complications often present challenges in optimization and alignment of the optics. It is not atypical for high-resolution sheet illumination systems to generate laser profiles with waist thicknesses approaching 900 nm. In order to optimize the overall image quality of the microscope, it is critical that the detective image plane coincide with this 900 nm laser thickness. Standard components used for positioning microscope objectives are often not designed for such precise, minimal translation; especially under human actuation. Additionally, stochastic variation in the biological geometry and position of the target specimen present issues to standard sheet illumination systems. Many model systems that are heavily imaged and researched in neuroscience and genetics, such as danio rerio and drosophila melanogaster, take a roughly spherical or cylindrical shape which act to defract and shift the plane of the laser itself in an unpredictable fashion. As such, our experimental aim is to develop a light-sheet feedback focusing system, with sub-micron translatory resolution, to optimize and fully leverage the benefits of sheet illumination, on a sample-by-sample level.

Background: 

In order to evaluate the practicality and viability of our light sheet autofocusing system, we decided to construct a simple testing platform with which we can evaluate and develop easily. In general, commercial sheet illumination microscopy systems from Zeiss and Leica are quite expensive and incompatible with modification, so we decided to construct our own. Within the community, a number of low-cost projects have been developed, as a means to make sheet illumination more accessible to the scientific community. The OpenSPIM [1], and LEGOLish [7] projects are among the most developed and experimentally viable; as such the light sheet autofocusing system’s opto-mechanical design was based on these existing platforms. One critical difference to the system we developed, as compared to more conventional geometries (such as OpenSPIM) is the definition of the position of the illuminative and detective objective lenses. Because the majority of SPIM imaging takes place through some type of biological media, the majority of systems make use of a fluid-filled sample chamber, in which the objectives are rigidly defined. In order to circumvent the issue of constructing a complicated watertight objective chamber, with a leak-proof seal capable of linear translation, we made use of a more unorthodox, upright SPIM geometry.

Read More

Polly Nor: Beyond Language

Art is a mechanism which provides a communication that surpasses language. 

I can feel what she means to say, despite being a guy. Theres something about the outward expression of a concept without spelling it out that does more than allow personal interpretation. I've heard the phrase more times than I'd like; regarding "multiple interpretations make art, artistic," and believe me, I get that. But I'm against it. 

Does the artist hold multiple self-inconsistent views of his/her own creation? 

Can other's interpretation be more valid than others? 

Opinion is contrary to empirical quantification. Being someone partial to scientific analysis may introduce bias, but it's hard to accept that all views exist on an infinite possibility plane, where all ideas are of equal worth. 

“Thinking About You. ”

Superpositus Extrema

In Mathematics, the two discrete maximum and minimum values of any function may be collectively referred to as the "Extrema." 

But I think that concept can be extended to represent my human condition because any experience, or collective range of experiences, may be assigned a number of characteristics which describe it. 

I find myself existing at both ends of that spectra simultaneously. 

That't to say that for any situation, there exists a counter condition - a sort of anti-situation which represents its inverse. The opposite of an inter-personal argument is probably a love poem, and the anti-situation of a death metal concert is most likely a Japanese Tea Garden. I often see these conditions as Extrema, in which people normally gravitate to either the maxima or minima, according to their persona. My personal case seems to flip in binary form, between extremes happily, where my net average tends toward 0.5. I'll eat vegan anti-meat one night, and the next get a five-piece "economy special" consisting of five fried chicken thighs from Roscoe's Chicken and Waffles on Pico and La Brea. I'll probably listen to Lamb of God and Dido on the way there. 

The discretization of the human condition would require more voxels than I could count; it certainly lies along a continuum. I just think that I might spend more time at either end than most. I'll work a 17 hour day then sleep until 2:00pm. I'll watch power-tool teardown videos on the internet, then bake cookies with Andes mints on them that I probably found on pinterest.  I have a favorite metal, it's Titanium. I think it's my favorite because it's strong and light, simultaneously. 

I'm a superposition of extrema. 

Coffees Of Los Angeles

I created a map of my favorite coffee shops in Los Angeles, where how red the marker is, is directly proportional to how much I enjoyed my experience there. I also have a coffee-inspired instagram: @coffee_papi

Research into the process. #coffee #latteart #espresso #la

A photo posted by @coffee_papi on

Studying with shortbread. #ucla #stumptown #coffee #espresso #la #study

A photo posted by @coffee_papi on

Research Runs on Coffee. ☕️ #stumptown #losangeles #ucla #research #coffee #espresso.

A photo posted by @coffee_papi on

Translations are just rotations about infinity.

Polynomial curve expressed in homogeneous coordinates (blue)

Polynomial curve expressed in homogeneous coordinates (blue)

Quite often small facts or thoughts have big impacts on me. 
The other day in my Electrical Engineering 209AS course, my Professor Ankur Mehta briefly and sort of nonchalantly pointed out that any translation of an object in any spatial dimension can simply be represented as a rotation about an axis positioned at infinity. 

While this was sort of a side note to his overall point regarding homologous coordinate systems and corresponding matrix transformations, I felt my mind slip into wonder at that satisfying thought. Such subtle intricacies of mathematics hold so much gravity about them when understood in the manor with which they deserve. Concepts of infinity and many-dimensional matrix transformations can often be difficult to fully comprehend and visualize innately. I believe it's through the small, somewhat quiet moments which one feels a connection to the universe, with the clicking of a small concept being employed. I swear that feeling is like the locking pins in a ratcheting mechanism, having just rotated past a new set of sprocket teeth. In the same way, it prevents one from rotating in the opposing direction - somehow as a means to prevent backward motion in understanding. 

The following is taken from wiki:Homogeneous Coordinates; read if you'd like, it's quite beautiful. 

The real projective plane can be thought of as the Euclidean plane with additional points added, which are called points at infinity, and are considered to lie on a new line, the line at infinity. There is a point at infinity corresponding to each direction (numerically given by the slope of a line), informally defined as the limit of a point that moves in that direction away from the origin. Parallel lines in the Euclidean plane are said to intersect at a point at infinity corresponding to their common direction. Given a point (x, y) on the Euclidean plane, for any non-zero real number Z, the triple (xZ, yZ, Z) is called a set of homogeneous coordinates for the point. By this definition, multiplying the three homogeneous coordinates by a common, non-zero factor gives a new set of homogeneous coordinates for the same point. In particular, (x, y, 1) is such a system of homogeneous coordinates for the point (x, y). For example, the Cartesian point (1, 2) can be represented in homogeneous coordinates as (1, 2, 1) or (2, 4, 2). The original Cartesian coordinates are recovered by dividing the first two positions by the third. Thus unlike Cartesian coordinates, a single point can be represented by infinitely many homogeneous coordinates.

Why I Listen to RADIOHEAD

Radiohead's seventh studio album, In Rainbows, was released on the 10th of October, 2007. At that time, I was a sophomore at my high school in Escondido, California - and I was under the impression that I understood a lot about music. 

At the time, my musical preferences were best personified by a schizophrenic homeless man, mainly because they shared a lot of acoustic similarity. I really enjoyed the type of music that involved discontinuous, incoherent yelling because at the time, that made up the majority of my mental state. Calling into question notions of power and control seem almost homologous to the distilled form of being a teenager. Listening to bands which hold similar principles at heart, like The Sex Pistols, The Clash, Rage Against the Machine, Iron Maiden and System of a Down, provided a reassuring confirmation to my rebellious internal state. It wasn't until the album In Rainbows released that I felt a change in my internal conception as a function of my external reassurance. 

 

My uncle, Bo, told me about the album which was to be released. Because he was my cool uncle that rode bicycles and drank weird teas, I decided to give it a shot, and I downloaded "In Rainbows" as soon as it came out. Strangely, the band made the album available through their website, on a "pay as you'd like" basis. Being fifteen I entered $0.00 into the field, and proceeded (weirdly) to downloading the album. From there, I simply installed it on my 4Gigabyte iPod touch, first generation, and took it with me to school. 

It wasn't until my Spanish class that something clicked. 

You see, my high school was a small charter-type school, and I was on the "independent-study" track. As such, I was required to walk to the community college nearby to complete a number of courses, because my high school simply did not have space for me to take them there. I was walking to my Spanish class when I started playing the album, I specifically remember the Taco Bell I was looking at as I pressed play. I had selected a track in the middle of the album, like an inpatient bafoon, hoping to cut right into the meaty part. The track is called "Nude" and I probably picked it because I was fifteen.

The mixing and composition of the first thirty seconds was enough to fully convince me that up to this point in my life, nothing more beautiful had touched my cochlea. As the track played, I fell ever-more deeply entranced by Thom's whimsical falsetto, only to be sharply removed from the spell thanks to my Spanish teacher's astounding mole on her left cheek. 

I honestly view those brief initial moments of hearing In Rainbows for the first time as the single most defining point in my understanding and love of music. Nothing since has felt as impactful, so mind-shatteringly brilliant that it left me questioning my own conception. That song, to me, was very important - not only in my mental interpretation of music what good music is, but on the capacity as to what music is capable of.