Biology subjects

Arisaka, K.

Publications and source records attributed to Arisaka, K..

6 recordsLinked to original sources

bioRxiv2026

Multimodal immobilization of second-instar Drosophila melanogaster larvae using PF-127 hydrogel and diethyl ether for calcium imaging

Motion artifacts remain a barrier to in vivo calcium imaging in Drosophila melanogaster larvae. Here, we evaluate a multimodal immobilization approach that combines a Pluronic F-127 (PF-127) hydrogel with brief diethyl ether vapor exposure (5 minutes, 25{degrees}C) and compare it against hydrogel-only immobilization using custom MATLAB-based analysis software that performs NoRMCorre rigid motion correction. In wide-field GFP recordings at 1 Hz over approximately 60 minutes (N = 15 per group), the multimodal condition significantly reduced motion across all three core metrics after FDR correction (all q < 0.001), with large effect sizes for mean speed (Hedges g = -1.18) and median step size (g = -1.36). In a secondary analysis of the first 30 minutes, uniformly large effect sizes (|g| = 1.10-1.51) were observed, consistent with stronger initial chemical immobilization that partially wanes over the recording period. We implemented a dual-flag quality control system that distinguishes motion data reliability from ROI detection eligibility. Control calcium recordings (33.33 Hz, [~]5 minutes; N = 23) yielded 368 ROIs with a mean SNR 30.4 {+/-} 16.9 and an event rate of 0.228 {+/-} 0.113 Hz. Experimental recordings (N = 21) yielded 295 ROIs with SNR 18.0 {+/-} 10.6 and event rate 0.309 {+/-} 0.188 Hz. SNR was higher in controls (Cliffs{delta} = 0.50, p < 0.001), while event rate was modestly higher in the experimental group at the ROI level ({delta} = -0.22, p < 0.001), though this difference did not reach significance at the sample level, suggesting altered but not suppressed calcium dynamics. These results support a practical, accessible immobilization workflow for larval calcium imaging. HighlightsO_LIBrief ether + hydrogel approach reduces larval motion 85-91% vs. hydrogel alone C_LIO_LIDual-flag QC system separates motion reliability from calcium ROI eligibility C_LIO_LICalcium event rates not suppressed under multimodal immobilization C_LIO_LIComplete MATLAB pipeline for motion analysis and calcium imaging provided C_LIO_LIAccessible protocol requires only standard laboratory supplies C_LI

neuroscience↗

bioRxiv2025

Transverse Sheet Illumination Microscopy (TranSIM): A High-Speed Platform for Large-Scale Volumetric Imaging

Recording the neural activity of biological organisms is paramount in understanding how they process the world around them. Fluorescence microscopy has served as the standard in recording this neural activity due to its ability to capture large populations of neurons simultaneously. Recent efforts in fluorescence microscopy have been concentrated in imaging large scale volumes, however, most of these efforts have been limited by spatiotemporal and bandwidth constraints. We present a novel system called Transverse-Sheet Illumination Microscopy (TranSIM), which captures spatially separated planes onto multiple two-dimensional sCMOS sensors at near diffraction limited resolution with 1.0 {micro}m, 1.4 {micro}m, and 4.3 {micro}m (x, y, and z respectively). The parallel use of sensors reduces the bandwidth bottlenecks typically found in other systems. TranSIM allows for the capturing of data at large-scale volumetric field-of-views up to 748 x 278 x 100 {micro}m3 at 100 Hz. Moreover, we were able to capture smaller field-of-views of 374 x 278 x 100 {micro}m3 at a faster volumetric rate of 200 Hz. Additionally, we found that the systems versatile design allowed us the ability to change the vertical magnification programmatically rather than necessitating a change of objectives. With this system we were able to observe intricate communication between neuron populations separated by vast three-dimensional distances, raising the potential to answer complex questions in Neurobiology.

bioengineering↗

bioRxiv2022

Visual Perception of 3D Space and Shape in Time - Part III: 2D Shape Recognition by Log-Scaling

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear with any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size and viewed from directly head on, the direct comparison between the one-sized memory and a new incoming image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly and reliably as we experience the objects in the world around us? Intriguingly, our primary visual cortex exhibits a 2D retinotopy with a log-polar coordinate system, where scaling up/down of shape is converted to linear frame translation. As a result, mental scaling can be performed by linearly translating the memory or the perceptual image until they overlap with each other. According to our new model of NHT (Neural Holography Tomography), alpha brainwaves traveling at a constant speed can conduct this linear translation. With this scheme, every scaling up/down by a factor of two should take the same amount of extra mental time to recognize a smaller/larger face. To test this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of unfamiliar faces with a given specific size (4{degrees} or 8{degrees}). Following the memorization phase, similar stimuli with a wide range of sizes (from 1{degrees} to 32{degrees}) were presented, and RTs were recorded. As predicted, the increase in RT was proportional to the scaling factor in the log scale. Furthermore, we observed that RTs were fastest for 8{degrees} faces even if the memorized face was 4{degrees}. This supports our hypothesis that we always memorize faces at the exact size of ~8 {degrees}. To our surprise, the increases in RT were also consistent with the mentally-estimated depth sensation, which indicates that the apparent size of the recognized face can create a proper depth sensation.

neuroscience↗

bioRxiv2022

Visual Perception of 3D Space and Shape In Time - Part IV: 3D Shape Recognition by 3D Rotation

Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear at any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size upfront at the object center, the direct comparison between the one-sized memory and an incoming new image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly as we experience it in our daily lives? This paper specifically addresses the recognition of human faces with arbitrary 3D orientation in the [Roll, Yaw, Pitch] axes. According to our new model of NHT (Neural Holography Tomography), space is represented by time utilizing the phase of the alpha brainwave. This principle should be applicable to any mental rotation in 3D; thus, it predicts that extra time is required to perceive a rotated face to revolve it back to upright by the constant-speed alpha wave. To assess this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of upright unfamiliar faces. Following the memorization phase, similar stimuli with a wide range of rotating faces in 3D were presented, and RTs were recorded. As expected, the memorized upfront face was the fastest RT. The excess of the RT was observed proportional to the rotating angle in all [Roll, Yaw, Pitch] axes. Roll had the flattest slope, whereas upper Pitch was the steepest. We suspect that Roll is the swiftest mental operation because it can be conducted by the linear frame translation on the log-polar retinotopy of the visual cortex.

neuroscience↗

bioRxiv2022

Visual Perception of 3D Space and Shape in Time - Part II: 3D Space Perception with Holographic Depth

Visual perception plays a critical role in navigating 3D space and extracting semantic information crucial to survival. Even though visual stimulation on the retina is fundamentally 2D, we seem to perceive the world around us in vivid 3D effortlessly. This reconstructed 3D space is allocentric and faithfully represents the external 3D world. How can we recreate stable 3D visual space so promptly and reliably? To solve this mystery, we have developed new concepts MePMoS (Memory-Prediction-Motion-Sensing) and NHT (Neural Holography Tomography). These models state that visual signal processing must be primarily top-down, starting from memory and prediction. Our brains predict and construct the expected 3D space holographically using traveling alpha brainwaves. Thus, 3D space is represented by the three time signals in three directions. To test this hypothesis, we designed reaction time (RT) experiments to observe predicted space-to-time conversion, especially as a function of distance. We placed LED strips on a horizontal plane to cover distances from close up to 2.5 m or 5 m, either using a 1D or a 2D lattice. Participants were instructed to promptly report observed LED patterns at various distances. As expected, stimulation at the fixation cue location always gave the fastest RT. Additional RT delays were proportional to the distance from the cue. Furthermore, both covert attention (without eye movements) and overt attention (with eye movements) created the same RT delays, and both binocular and monocular views resulted in the same RTs. These findings strongly support our predictions, in which the observed RT-depth dependence is indicative of the spatiotemporal conversion required for constructing allocentric 3D space. After all, we perceive and measure 3D space by time as Einstein postulated a century ago.

neuroscience↗

bioRxiv2020

Visual Perception in the Periphery: The Role of Covert Attention Vectors in the Extraction of Semantic Information

Under covert attention, our visual perception deteriorates dramatically as eccentricity increases. This reduction of peripheral visual acuity (PVA) is partially due to the coarse sampling of the retinal ganglion cells towards the periphery, but this property cannot be solely responsible. Other factors, such as character crowding, have been studied, yet the origin of the poor PVA is not entirely understood. This gap motivated us to investigate the PVA by varying the crowding conditions systematically. Under completely crowded conditions (i.e. resembling a full page of text), PVA was observed to be eight times worse than the PVA under uncrowded conditions. By partially crowding the periphery, we obtained PVA values between the fully crowded and uncrowded conditions. On the other hand, crowding the fovea center while leaving the periphery uncrowded improved PVA relative to the uncrowded case. These results support a model for a top-down "covert attention vector" that assists the resulting PVA in a manner analogous to saccadic eye movement for overt attention. We speculate that the attention vector instructs the dorsal pathway to transform the peripheral character to the foveal center. Then, the scale-invariant log-polar retinotopy of the ventral pathway can scale the centered visual input to match the prior memory of the specific character shape.

neuroscience↗