Murthy - Revision history

imported>Student221: /* Control Model Trends */

2019-12-13T22:41:35Z

Control Model Trends

← Older revision		Revision as of 22:41, 13 December 2019
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	When running the control model with 50 fixational eye movements per trial, for 100 trials, the MTF output is in Figure 7 below. It is clear that the MTFs vary considerably in the higher spatial frequency portions of the plot. However, the MTF50 value remained fairly consistent, which can be seen in Figure 7 as well. The mean MTF50 was '''7.51 cyc/deg''' for this scenario, and the standard deviation was 0.7674 cyc/deg. This indicates visual acuity markedly decreased with fixational eye movements.		When running the control model with 50 fixational eye movements per trial, for 100 trials, the MTF output is in Figure 7 below. It is clear that the MTFs vary considerably in the higher spatial frequency portions of the plot. However, the MTF50 value remained fairly consistent, which can be seen in Figure 7 as well. The mean MTF50 was '''7.51 cyc/deg''' for this scenario, and the standard deviation was 0.7674 cyc/deg. This indicates visual acuity markedly decreased with fixational eye movements.

	[[File:Fixational.png\|~~700px~~\|thumb\|center\| Figure 7: (Left) All MTFs for control model with fixational eye movements and no photon noise. (Right) MTF50 for all trials.]]		[[File:Fixational.png\|800px\|thumb\|center\| Figure 7: (Left) All MTFs for control model with fixational eye movements and no photon noise. (Right) MTF50 for all trials.]]

	This finding agrees with Martinez-Conde et. al. and their fatigue theory [7]. To investigate whether fatigue could have occurred, I briefly looked at the cone photocurrent values on the first and last time step for the scenario without eye movements. The mean photocurrent absorptions were approximately the same for each (both were ~45), which indicates photoreceptor fatigue was not built into the ISETBio model.		This finding agrees with Martinez-Conde et. al. and their fatigue theory [7]. To investigate whether fatigue could have occurred, I briefly looked at the cone photocurrent values on the first and last time step for the scenario without eye movements. The mean photocurrent absorptions were approximately the same for each (both were ~45), which indicates photoreceptor fatigue was not built into the ISETBio model.
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	When investigating the Nystagmus patterns, again with 50 eye movements and 100 trials, it was found that the mean absorption image was greatly affected by the orientation of the eye movements in relation to the slanted edge. The more perpendicular the movement was to the edge, the greater the blur effect in the absorption image. This is demonstrated in Figure 8 below.		When investigating the Nystagmus patterns, again with 50 eye movements and 100 trials, it was found that the mean absorption image was greatly affected by the orientation of the eye movements in relation to the slanted edge. The more perpendicular the movement was to the edge, the greater the blur effect in the absorption image. This is demonstrated in Figure 8 below.

	[[File:Nystagmus blurs final.png\|~~1000px~~\|center\|thumb\| Figure 8: Mean Cone Absorption Images for Control Model with no photon noise and various nystagmus orientations. Note that the blur increases as the nystagmus orientation grows closer to perpendicular to the slanted edge.]]		[[File:Nystagmus blurs final.png\|1100px\|center\|thumb\| Figure 8: Mean Cone Absorption Images for Control Model with no photon noise and various nystagmus orientations. Note that the blur increases as the nystagmus orientation grows closer to perpendicular to the slanted edge.]]

	Logically, this blur effect had an effect on the resultant MTFs. The photon noise-less MTFs for the two extremes, the parallel and perpendicular nystagmus movements, are in Figure 9. It is clear to see that the parallel MTF closely resembles the benchmark no-movement MTF in Figure 6. However, the perpendicular MTF suffers a rapid decline in contrast, and has an MTF50 value of approximately half that of the parallel. This indicates that one’s visual acuity with respect to an edge in an image depend on the orientation of one’s eye movements in relation to that edge.		Logically, this blur effect had an effect on the resultant MTFs. The photon noise-less MTFs for the two extremes, the parallel and perpendicular nystagmus movements, are in Figure 9. It is clear to see that the parallel MTF closely resembles the benchmark no-movement MTF in Figure 6. However, the perpendicular MTF suffers a rapid decline in contrast, and has an MTF50 value of approximately half that of the parallel. This indicates that one’s visual acuity with respect to an edge in an image depend on the orientation of one’s eye movements in relation to that edge.

imported>Student221: /* Generating Eye Movement Sequences */

2019-12-13T22:40:56Z

Generating Eye Movement Sequences

← Older revision		Revision as of 22:40, 13 December 2019
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	Finally, the drift sequence was added. For this sequence, it is only horizontal, and there is no jitter involved. One can specify an amplitude in cones of the mosaic, and the eye will drift to the positive and negative of that amplitude, but will only do this once over the entire course of the movement sequence. This is a much slower movement in relation to the nystagmus movements. The difference between the drift and nystagmus sequence can be seen in Figure 5 below.		Finally, the drift sequence was added. For this sequence, it is only horizontal, and there is no jitter involved. One can specify an amplitude in cones of the mosaic, and the eye will drift to the positive and negative of that amplitude, but will only do this once over the entire course of the movement sequence. This is a much slower movement in relation to the nystagmus movements. The difference between the drift and nystagmus sequence can be seen in Figure 5 below.

	[[File:Drift final.gif\|~~350px~~\|left\| Figure 5a: Horizontal Drift eye movement representation with cone absorptions.]] [[File:Nystagmus final.gif\|~~350px~~\|center\| Figure 5b: Horizontal Nystagmus eye movement representation with cone absorptions.]]		[[File:Drift final.gif\|600px\|thumb\|left\| Figure 5a: Horizontal Drift eye movement representation with cone absorptions.]] [[File:Nystagmus final.gif\|600px\|thumb\|center\| Figure 5b: Horizontal Nystagmus eye movement representation with cone absorptions.]]

	=== Automated Script ===		=== Automated Script ===

imported>Student221: /* Generating Eye Movement Sequences */

2019-12-13T22:39:46Z

Generating Eye Movement Sequences

← Older revision		Revision as of 22:39, 13 December 2019
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	Finally, the drift sequence was added. For this sequence, it is only horizontal, and there is no jitter involved. One can specify an amplitude in cones of the mosaic, and the eye will drift to the positive and negative of that amplitude, but will only do this once over the entire course of the movement sequence. This is a much slower movement in relation to the nystagmus movements. The difference between the drift and nystagmus sequence can be seen in Figure 5 below.		Finally, the drift sequence was added. For this sequence, it is only horizontal, and there is no jitter involved. One can specify an amplitude in cones of the mosaic, and the eye will drift to the positive and negative of that amplitude, but will only do this once over the entire course of the movement sequence. This is a much slower movement in relation to the nystagmus movements. The difference between the drift and nystagmus sequence can be seen in Figure 5 below.

	[[File:Drift final.gif\|350px~~\|thumb~~\|left\| Figure 5a: Horizontal Drift eye movement representation with cone absorptions.]] [[File:Nystagmus final.gif\|350px~~\|thumb~~\|center\| Figure 5b: Horizontal Nystagmus eye movement representation with cone absorptions.]]		[[File:Drift final.gif\|350px\|left\| Figure 5a: Horizontal Drift eye movement representation with cone absorptions.]] [[File:Nystagmus final.gif\|350px\|center\| Figure 5b: Horizontal Nystagmus eye movement representation with cone absorptions.]]

	=== Automated Script ===		=== Automated Script ===

imported>Student221: /* References */

2019-12-13T22:38:10Z

References

← Older revision		Revision as of 22:38, 13 December 2019
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	== References ==		== References ==

	[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094591/ Link]		[1] – Kowler, Eileen. “Eye movements: The past 25 years.” ''Vision Research''. 2011. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094591/ Link]

	[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018. [https://link-springer-com.stanford.idm.oclc.org/article/10.1007/s12311-017-0910-5 Link]		[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” ''The Cerebullum''. 2018. [https://link-springer-com.stanford.idm.oclc.org/article/10.1007/s12311-017-0910-5 Link]

	[3] – The Stanford Artificial Retina Project. 2019. [http://med.stanford.edu/artificial-retina/research.html Link]		[3] – The Stanford Artificial Retina Project. 2019. [http://med.stanford.edu/artificial-retina/research.html Link]

	[4]- ISETBio.		[4]- Wandell, Brian et al. ISETBio. [https://github.com/isetbio/isetbio Github Link]

	[5]- Zheng et. al. “Analysis of the optical quality by determining the modulation transfer function for anterior corneal surface in myopes.” International Journal of Opthalmology. 2012		[5]- Zheng et. al. “Analysis of the optical quality by determining the modulation transfer function for anterior corneal surface in myopes.” ''International Journal of Opthalmology''. 2012. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359037/ Link]

	[6] – Foundations of Vision		[6] – Wandell, Brian A. ''Foundations of Vision''. [https://foundationsofvision.stanford.edu/ Link]

	[7]- Martinez-Conde, Susana et. al. “The Role of Fixational Eye Movements in Visual Perception.” Nature Reviews: Neuroscience. 2004.		[7]- Martinez-Conde, Susana et. al. “The Role of Fixational Eye Movements in Visual Perception.” ''Nature Reviews: Neuroscience''. 2004. [https://www-nature-com.stanford.idm.oclc.org/articles/nrn1348.pdf Link]

	[8]- Yao, Jun-Ping et al. “A new measure of nystagmus acuity.” International Journal of Opthalmology. 2014.		[8]- Yao, Jun-Ping et al. “A new measure of nystagmus acuity.” ''International Journal of Opthalmology''. 2014. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949466/ Link]
	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949466/

	[9]- Estribeau, M. and Magnan, P. “Fast MTF measurement of CMOS imagers using ISO 12233 slanted-edge methodology.” Integrated Sensors Laboratory.		[9]- Estribeau, M. and Magnan, P. “Fast MTF measurement of CMOS imagers using ISO 12233 slanted-edge methodology.” ''Integrated Sensors Laboratory''. [https://core.ac.uk/download/pdf/12039012.pdf Link]
	https://core.ac.uk/download/pdf/12039012.pdf

	[10]-Curcio et al. “Human Photoreceptor Topography.” The Journal of Comparative Neurology. 1990.		[10]- Curcio et al. “Human Photoreceptor Topography.” ''The Journal of Comparative Neurology''. 1990. [https://onlinelibrary-wiley-com.stanford.idm.oclc.org/doi/epdf/10.1002/cne.902920402 Link]
	https://onlinelibrary-wiley-com.stanford.idm.oclc.org/doi/epdf/10.1002/cne.902920402

	== Appendix ==		== Appendix ==

imported>Student221: /* References */

2019-12-13T22:30:36Z

References

← Older revision		Revision as of 22:30, 13 December 2019
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	[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094591/ Link]		[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094591/ Link]

	[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018		[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018. [https://link-springer-com.stanford.idm.oclc.org/article/10.1007/s12311-017-0910-5 Link]

	[3] – Stanford Artificial Retina		[3] – The Stanford Artificial Retina Project. 2019. [http://med.stanford.edu/artificial-retina/research.html Link]

	[4]- ISETBio.		[4]- ISETBio.

imported>Student221: /* References */

2019-12-13T22:28:20Z

References

← Older revision		Revision as of 22:28, 13 December 2019
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	== References ==		== References ==

	[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011		[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094591/ Link]

	[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018		[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018

imported>Student221: /* Generating Cone Mosaics */

2019-12-13T22:27:09Z

Generating Cone Mosaics

← Older revision		Revision as of 22:27, 13 December 2019
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	Second, the “'''periphery'''” model was created. This cone mosaic is intended to represent the photoreceptors at a few degrees eccentricity relative to the center of the fovea. Initially, I considered making a mosaic that included blank spaces, which would represent rods. However, when attempting to run the ISO12233 routine using a model with blank cones, the resultant MTFs either failed to compute or had erroneous shapes, indicating computational difficulty.		Second, the “'''periphery'''” model was created. This cone mosaic is intended to represent the photoreceptors at a few degrees eccentricity relative to the center of the fovea. Initially, I considered making a mosaic that included blank spaces, which would represent rods. However, when attempting to run the ISO12233 routine using a model with blank cones, the resultant MTFs either failed to compute or had erroneous shapes, indicating computational difficulty.

	To address this issue while still attempting to generate a relatively accurate retinal model, the periphery model was chosen to represent '''2 degrees of eccentricity'''. This decision was based on [https://foundationsofvision.stanford.edu/wp-content/uploads/2012/02/rod.cone_.distribution2.png Figure 3.1 from ''Foundations of Vision''] (linked) [6], which depicts the density of rods and cones as one moves across the retina. It is clear to see that while cone density falls off rapidly as one moves peripherally from the fovea, there is still a high concentration of cones at 2 degrees of eccentricity. To determine the aperture size for these cones, the ISETBio function “coneSizeReadData” was used. This function uses data from Curcio et. al. (Figure 6), in Figure 2 below, to estimate cone aperture size from cone density data [9]. Using this method, the cone '''aperture size for the periphery model was 3.89 micron'''. The relative density of L, M, and S cones is 60%, 30%, and 10% respectively, based off a claim in ''Foundations of Vision'' [6]. This mosaic is also depicted in Figure 3 below.		To address this issue while still attempting to generate a relatively accurate retinal model, the periphery model was chosen to represent '''2 degrees of eccentricity'''. This decision was based on [https://foundationsofvision.stanford.edu/wp-content/uploads/2012/02/rod.cone_.distribution2.png Figure 3.1 from ''Foundations of Vision''] (linked) [6], which depicts the density of rods and cones as one moves across the retina. It is clear to see that while cone density falls off rapidly as one moves peripherally from the fovea, there is still a high concentration of cones at 2 degrees of eccentricity. To determine the aperture size for these cones, the ISETBio function “coneSizeReadData” was used. This function uses data from Curcio et. al. (Figure 6), in Figure 2 below, to estimate cone aperture size from cone density data [10]. Using this method, the cone '''aperture size for the periphery model was 3.89 micron'''. The relative density of L, M, and S cones is 60%, 30%, and 10% respectively, based off a claim in ''Foundations of Vision'' [6]. This mosaic is also depicted in Figure 3 below.

	[[File:Curcio.png\|400px\|thumb\|left\| Figure 2: Cone Density Data from Curcio et. al. [9]]] [[File:Mosaics.png\|600px\|thumb\|center\|Figure 3: Cone Mosaic Models. (Left) "Center" model. (Right) "Periphery" Model.]]		[[File:Curcio.png\|400px\|thumb\|left\| Figure 2: Cone Density Data from Curcio et. al. [10]]] [[File:Mosaics.png\|600px\|thumb\|center\|Figure 3: Cone Mosaic Models. (Left) "Center" model. (Right) "Periphery" Model.]]

	=== Generating Eye Movement Sequences ===		=== Generating Eye Movement Sequences ===

imported>Student221: /* References */

2019-12-13T22:26:37Z

References

← Older revision		Revision as of 22:26, 13 December 2019
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	https://core.ac.uk/download/pdf/12039012.pdf		https://core.ac.uk/download/pdf/12039012.pdf

	[9]-Curcio et al. “Human Photoreceptor Topography.” The Journal of Comparative Neurology. 1990.		[10]-Curcio et al. “Human Photoreceptor Topography.” The Journal of Comparative Neurology. 1990.
	https://onlinelibrary-wiley-com.stanford.idm.oclc.org/doi/epdf/10.1002/cne.902920402		https://onlinelibrary-wiley-com.stanford.idm.oclc.org/doi/epdf/10.1002/cne.902920402

imported>Student221: /* References */

2019-12-13T22:26:19Z

References

← Older revision		Revision as of 22:26, 13 December 2019
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	== References ==		== References ==

			[1] – Kowler, Eileen. “Eye movements: The past 25 years.” Vision Research. 2011

			[2] – Shaikh, Aasef G. and Zee, David S. “Eye Movement Research in the Twenty-First Century—a Window to the Brain, Mind, and More.” The Cerebullum. 2018

			[3] – Stanford Artificial Retina

			[4]- ISETBio.

			[5]- Zheng et. al. “Analysis of the optical quality by determining the modulation transfer function for anterior corneal surface in myopes.” International Journal of Opthalmology. 2012

			[6] – Foundations of Vision

			[7]- Martinez-Conde, Susana et. al. “The Role of Fixational Eye Movements in Visual Perception.” Nature Reviews: Neuroscience. 2004.

			[8]- Yao, Jun-Ping et al. “A new measure of nystagmus acuity.” International Journal of Opthalmology. 2014.
			https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949466/

			[9]- Estribeau, M. and Magnan, P. “Fast MTF measurement of CMOS imagers using ISO 12233 slanted-edge methodology.” Integrated Sensors Laboratory.
			https://core.ac.uk/download/pdf/12039012.pdf

			[9]-Curcio et al. “Human Photoreceptor Topography.” The Journal of Comparative Neurology. 1990.
			https://onlinelibrary-wiley-com.stanford.idm.oclc.org/doi/epdf/10.1002/cne.902920402

	== Appendix ==		== Appendix ==

imported>Student221: /* Limitations and Future Work */

2019-12-13T22:25:29Z

Limitations and Future Work

← Older revision		Revision as of 22:25, 13 December 2019
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	===Limitations and Future Work===		===Limitations and Future Work===

	One major limitation of this investigation was the fact that the cone mosaic pattern was generated randomly for each individual movement type. For example, the center model mosaic for the fixational eye movements was different than the one for drift eye movements. This is not ideal for a controlled experiment, as ~~people~~ only have one mosaic ~~each~~. The results presented here therefore implicitly assume that the relative distribution of cone types matters more than the specific location of those cones in the mosaic.		One major limitation of this investigation was the fact that the cone mosaic pattern was generated randomly for each individual movement type. For example, the center model mosaic for the fixational eye movements was different than the one for drift eye movements. This is not ideal for a controlled experiment, as one person's eye would only have one mosaic. The results presented here therefore implicitly assume that the relative distribution of cone types matters more than the specific location of those cones in the mosaic.

	Another limitation was the computational challenge that occurred with the ISO12233 routine. A future project might investigate if there is a way to improve that script, potentially enabling this investigation with a retinal model that has blank spaces to represent rods.		Another limitation was the computational challenge that occurred with the ISO12233 routine. A future project might investigate if there is a way to improve that script, potentially enabling this investigation with a retinal model that has blank spaces to represent rods.