Merge branch 'gulpinhenry-master'

docs/course/visual_perception.md

@@ -1,32 +1,58 @@
-# Visual Perception
-
-:octicons-info-24: Informative
-
-This section of `Computational Light course` introduces various components of human vision system, which plays a critical role in the design of camera, compute and display systems.
-
 ## Color Perception
 
-:octicons-info-24: Informative
+We can establish an understanding on color perception through studying its physical and perceptual meaning.
+This way, we can gather more information on its relation to technologies and devices including displays, cameras, sensors, communication, computing and computer graphics.
 
-We can establish an understanding on color perception through studying its physical and perceptual meaning, so we can understand motivations behind display, computer graphic and camera technologies.
-Color can be explained in a physical and perceptual capacity. In the physical sense, color is a quantity typically described using a wavelength of light. Humans can only percieve color within a certain range of the electromagnetic spectrum, from around 400 to 700 nanometers. For greater details on the electromagnetic spectrum and concept of wavelength, we recommend revisiting [Light, Computation, and Computational Light](computational_light.md) section of our course. Color is a perceptual phenomenon arising from the human visual system's interaction with light. Color is essentially a "side effect" created by our brain when specific wavelengths of light are emitted, reflected, or transmitted by objects.
+### What is Color?
 
-The perception of color originates from the absorption of light by photoreceptors in the eye, converting the light into electrical signals to be interpreted by the brain. 
+Color, a perceptual phenomenon, can be explained in a physical and visual perception capacity.
+In the physical sense, color is a quantity representing the response to wavelength of light.
+Humans visual system can percieve colors within a certain range of the electromagnetic spectrum, from around 400 nanometers to 700 nanometers.
+For greater details on the electromagnetic spectrum and concept of wavelength, we recommend revisiting [Light, Computation, and Computational Light](computational_light.md) section of our course.
+Color is also a perceptual concept arising from the human visual system's interaction with wavelengths of light.
+Color is essentially a "side effect" created by our brain when specific wavelengths of light are emitted, reflected, or transmitted by objects.
+The perception of color originates from the absorption of light by photoreceptors in the eye, converting the light into electrical signals to be interpreted by the brain[^1].
+Here, you can see a close-up photograph of these photoreceptor cells found in the eye.
 
-This note will only discuss the role of our eyes; for more information about how brain percieves light, please refer to [this paper](https://pubmed.ncbi.nlm.nih.gov/21841776/)
+<figure markdown>
+  ![Image title](media/rods_and_cones_closeup.jpg){ width="600" }
+  <figcaption>Live Capture of Photoreceptor Cells (CC PDM 1.0 by NIH).</figcaption>
+</figure>
 
-The photoreceptors where color perception originates are called [rods and cones](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763127/). Rods, which are relatively more common in the periphery, help people see in low-light conditions, but can only interpret in a greyscale manner. Cones, which are more dense in the fovea, are pivotal in color perception in relatively normal environments. The cones are categorized into three types based on their sensitivity to specific wavelengths of light, corresponding to long (L), medium (M), and short (S) wavelengths. These [three types of cones](https://opg.optica.org/josaa/fulltext.cfm?uri=josaa-31-4-A195&id=279354) allow us to better understand the [trichromatic theory](https://www.jstor.org/stable/82365), which suggests that human color perception stems from combining stimulations of the LMS cones, which correspond to red, green, and blue light, respectively. For example, red is perceived when L cones are significantly stimulated more than the other types, and blue is perceived when S cone activation is more prominent. Scientists have tried to graphically represent how sensitive each type of cone is to different wavelengths of light, which is known as the spectral sensitivity function.
+The photoreceptors, where color perception originates, are called [rods and cones](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763127/)[^3]. 
+Here, we provide a sketch showing where these rods and cones are located inside the eye.
+By closely observing this sketch, you can also understand the basic average geometry of a human eye and its parts that helps redirect light from an actual scene towards retinal cells.
 
-??? question end "Would you like to learn more about LMS?"
-       Check out [this paper: B. P. Schmidt, M. Neitz, and J. Neitz, "Neurobiological hypothesis of color appearance and hue perception," J. Opt. Soc. Am. A 31(4), A195–207 (2014)](https://europepmc.org/article/pmc/4167798)! 
+<figure markdown>
+  ![Image title](media/photoreceptors_rods_and_cones.png){ width="600" }
+  <figcaption>Anatomy of an Eye (Designed with BioRender).</figcaption>
+</figure>
+
+Rods, which are relatively more common in the periphery, help people see in low-light (scotopic) conditions, but can only interpret in a greyscale manner. Cones, which are more dense in the fovea, are pivotal in color perception in brighter (photopic) environments. 
+We highlight the distribution of these photoreceptor cells, rods and cones with changing eccentricities in the eye.
+<figure markdown>
+  ![Image title](media/retinal_photoreceptor_distribution.png){ width="600" }
+  <figcaption>Retinal Photoreceptor Distribution, adapted from the work by Goldstein et al [3].</figcaption>
+</figure>
+In the above sketch, we introduced various parts on the retina, including fovea, parafovea, perifovea and peripheral vision.
 
 
 <figure markdown>
   ![Image title](media/lms_graph.png){ width="600" }
   <figcaption>Spectral Sensitivities of LMS cones</figcaption>
 </figure>
 
-However, the story of color perception deepens with the concept of [color opponency](https://pubmed.ncbi.nlm.nih.gov/1303712/). This theory reveals that our perception of color is not just a matter of additive combinations of primary colors but also involves a dynamic interplay of opposing colors: red versus green, blue versus yellow. This phenomenon is rooted in the neural pathways of the eye and brain, where certain cells are excited or inhibited by specific wavelengths, enhancing our ability to distinguish between subtle shades and contrasts.
+The cones are categorized into three types based on their sensitivity to specific wavelengths of light, corresponding to long (L), medium (M), and short (S) wavelength cones. These [three types of cones](https://opg.optica.org/josaa/fulltext.cfm?uri=josaa-31-4-A195&id=279354)[^4] allow us to better understand the [trichromatic theory](https://www.jstor.org/stable/82365)[^5], suggesting that human color perception stems from combining stimulations of the LMS cones. Scientists have tried to graphically represent how sensitive each type of cone is to different wavelengths of light, which is known as the spectral sensitivity function[^6].
+??? question end "Looking for more reading to expand your understanding on human visual system?"
+       We recommend these papers, which we find it insightful:
+       - [ B. P. Schmidt, M. Neitz, and J. Neitz, "Neurobiological hypothesis of color appearance and hue perception," J. Opt. Soc. Am. A 31(4), A195–207 (2014)](https://doi.org/10.1364/josaa.31.00a195)
+       - [Biomimetic Eye Modeling & Deep Neuromuscular Oculomotor Control](https://www.andrew.cmu.edu/user/aslakshm/pdfs/siggraph19_eye.pdf)
+
+
+The story of color perception only deepens with the concept of [color opponency](http://dx.doi.org/10.1364/JOSAA.34.001099)[^7]. This theory reveals that our perception of color is not just a matter of additive combinations of primary colors but also involves a dynamic interplay of opposing colors: red versus green, blue versus yellow. This phenomenon is rooted in the neural pathways of the eye and brain, where certain cells are excited or inhibited by specific wavelengths, enhancing our ability to distinguish between subtle shades and contrasts.
+
+??? question end "How can I find the LMS response of an image using odak?"
+       Check out this [engineering note](../notes/color_perception.md)! 
 
 
 ### Display Realism (What does it mean to be realistic)
@@ -56,6 +82,12 @@ Human perception is extremely context dependent, where we need to adapt to vario
 As we dive deeper into light and color perception, it becomes evident that the task of replicating the natural spectrum of colors in technology is still an evolving journey. This exploration into the nature of color sets the stage for a deeper examination of how our biological systems perceive color and how technology strives to emulate that perception.
 
 
-## Color Science
-[Biomimetic Eye Modeling & Deep Neuromuscular Oculomotor Control](https://www.andrew.cmu.edu/user/aslakshm/pdfs/siggraph19_eye.pdf)
+[^1]: [Freeman, J. and Simoncelli, E.P. 2011. Metamers of the ventral stream. Nature Neuroscience 14, 1195–1201. http://dx.doi.org/10.1038/nn.2889.](https://doi.org/10.1038/nn.2889)
+[^2]: [Cleveland Clinic. 2024. Photoreceptors (Rods and Cones). Cleveland Clinic. Accessed September 27, 2024. https://my.clevelandclinic.org/-/scassets/images/org/health/articles/photoreceptors-rods-and-cones.](https://my.clevelandclinic.org/-/scassets/images/org/health/articles/photoreceptors-rods-and-cones)
+[^3]: [GOLDSTEIN E. B.: Sensation and Perception, 8th ed. Wadsworth-Thomson Learning, Pacific Grove, 2010.](https://psycnet.apa.org/record/1988-98693-000)
+[^4]: [Lamb, T.D. 2015. Why rods and cones? Eye 30, 179–185. http://dx.doi.org/10.1038/eye.2015.236.](https://doi.org/10.1038/eye.2015.236)
+[^5]: [Schmidt, B.P., Neitz, M., and Neitz, J. 2014. Neurobiological hypothesis of color appearance and hue perception. Journal of the Optical Society of America A 31, A195. http://dx.doi.org/10.1364/JOSAA.31.00A195.](https://doi.org/10.1364/JOSAA.31.00A195)
+[^6]: [Some experiments on the trichromatic theory of vision. 1942. Proceedings of the Royal Society of London. Series B - Biological Sciences 131, 27–50. http://dx.doi.org/10.1098/rspb.1942.0016.](https://doi.org/10.1098/rspb.1942.0016)
+[^7]: [Stockman, A. and Sharpe, L.T. 2000. The spectral sensitivities of the middle- and long-wavelength-sensitive cones derived from measurements in observers of known genotype. Vision Research 40, 1711–1737. http://dx.doi.org/10.1016/S0042-6989(00)00021-3.](https://doi.org/10.1016/S0042-6989(00)00021-3)
+[^8]: [Shevell, S.K. and Martin, P.R. 2017. Color opponency: tutorial. Journal of the Optical Society of America A 34, 1099. http://dx.doi.org/10.1364/JOSAA.34.001099.](http://dx.doi.org/10.1364/JOSAA.34.001099)