diff --git "a/CtFJT4oBgHgl3EQfAiym/content/tmp_files/load_file.txt" "b/CtFJT4oBgHgl3EQfAiym/content/tmp_files/load_file.txt" new file mode 100644--- /dev/null +++ "b/CtFJT4oBgHgl3EQfAiym/content/tmp_files/load_file.txt" @@ -0,0 +1,616 @@ +filepath=/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf,len=615 +page_content='Non-invasive and noise-robust light focusing using confocal wavefront shaping Dror Aizik, Anat Levin Department of Electrical and Computer Engineering, Technion, Haifa, Israel Abstract One of the hardest barriers to our ability to see inside biological tissue is the fact that light is highly aberrated when scattering by the tissue sub-components.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' One of the promising approaches for overcoming such aberrations is wavefront-shaping, where one modulates the incoming and/or the outgoing wavefront in a way that will allow it to focus into one spot despite scattering in the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Wavefront modulations are specific to the tissue sample being imaged and need to be estimated based on a non- invasive feedback from a camera collecting back-scattered light.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Such modulations have been successively estimated using feedback from strong fluorescent beads which have been manually added to a sample.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, in a real biomedical application, such feedback should be provided by the fluorescent components of the tissue itself, whose emission is orders of magnitude lower than the one pro- vided by beads.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' When such a low number of photons is spread over multiple sensor pixels, the image is highly susceptible to noise, and the feedback signal required for previous algorithms cannot be detected.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In this work we suggest a wavefront shaping approach that works with a confocal modulation of both illumina- tion and imaging arms.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The advantage of this approach is that as part of the optimization, aberrations are corrected in the optics, before the detector.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Hence the low photon budget can be directed into a single sensor spot and de- tected with high SNR.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We derive the optimization prob- lem from mathematical principles and show why it favors modulations that actually correct the aberrations and fo- cus all light into one spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We successfully demonstrate wavefront-shaping correction on EGFP neurons sliced out of a mouse brain, despite scattering through thick tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 1 Introduction One of the hardest barriers to light-based approaches to tissue imaging is the fact that light is heavily scattered due to variations in the refractive index of tissue struc- tures.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A promising approach for overcoming the scatter- ing challenge is a wavefront-shaping based correction.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' By using a spatial light modulator (SLM) device, one can reshape the coherent wavefront illuminating the sample, such that its aberration is conjugate to the aberration that will happen inside the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' When such a wavefront propagates through the sample, all incoming light can be brought (focused) into a small spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In the same way, by using a wavefront modulation element between the tissue and the sensor, we can correct the outgoing wavefront, so that light photons emerging from a single target point are brought into a single sensor point, despite the tissue aberration.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The main advantage of this approach results from the fact that unlike ballistic-filtering approaches, all light photons are used.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Earlier wavefront shaping approaches, formally known as adaptive optics [5, 12, 15], were first used to correct modest aberrations, for example due to imperfect optics or refractive index variations in the tissue [6,16,31].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' More recently, wavefront shaping techniques [11, 13, 37] have shown that it is possible to focus light through thick, highly-scattering layers [28–30,35].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Despite the large potential of the idea, finding the de- sired shape of the modulation correction is rather chal- lenging.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The desired modulation varies between different tissue samples and even varies spatially between different positions of the same tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For thick tissue, the modu- lation is a complex pattern containing a large number of free modes.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Earlier proof-of-concept demonstrations have used a validation camera behind the tissue to provide feed- back to the algorithm [7, 8, 24, 29, 30, 35], and other approaches have relied on the existence of a guiding- star [10, 13, 14, 18–20, 27, 28, 32–34].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In the absence of such a guiding star, and when only non-invasive feed- back is available, determining whatever a wavefront has focused inside the tissue is not straightforward.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The dif- ficulty results from the fact that even if we can find an illumination wavefront that actually focuses into a small spot inside the tissue, the light back-scattering from this 1 arXiv:2301.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='11421v1 [physics.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='optics] 26 Jan 2023 spot is aberrated again on its way to the camera, forming yet another scattered pattern.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The simplest way to evaluate whatever a wavefront modulation has focused is to use multi-photon fluores- cence feedback.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In this way, the light emitted from a flu- orescence spot is a non-linear function of the excitation intensity arriving it, so when all light is focused into a sin- gle spot the total emission energy is maximized [15, 18].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, obtaining feedback using single-photon fluores- cence is highly desired as the process is significantly sim- pler and cheaper than the multi-photon one.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The single- photon case cannot be evaluated using the simple score function applied in the multi-photon case, since the emis- sion energy is a linear function of the excitation energy and thus the amount of emission energy does not increase when all excitation is focused into a spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Recently, progress has been made on non-invasive wave- front shaping using single-photon feedback [1, 3].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' First, Boniface et al.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [3] have suggested that one can evalu- ate whatever an incoming wavefront modulation has fo- cused by computing the variance of the emitted speckle pattern.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' More recently, Aizik et al.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [1] has suggested a rapid approach that can find a wavefront shaping mod- ulation using a small number of iterative phase conjuga- tion iterations.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Both approaches were only demonstrated when the fluorescent feedback was provided by synthetic fluorescent beads, which emit a relatively strong signal.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, the ultimate goal is to apply wavefront shap- ing modulation using feedback from biological samples, such as neurons.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The signal emitted from such samples is orders of magnitude weaker than the one provided by fluorescent beads, and bleaching is reached much earlier.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Both algorithms [1,3] inherently assume that the speckle pattern emitted from a single fluorescent spot can be mea- sured.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, the number of fluorescent photons emit- ted from a neuron spot is so low that when these photons are aberrated and spread over multiple sensor pixels, no speckle pattern can be observed and one can mostly mea- sure noise, see visualization in Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' With such a low photon count no speckle variance can be estimated as is required by [3], and no phase retrieval process can be ro- bustly carried as in [1].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This work proposes a wavefront shaping framework that can apply in low-light scenarios and use feedback from realistic biological data.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' To this end, we propose to use a simultaneous wavefront shaping modulation both on the incoming excitation wavefront and on the outgo- ing emitted light.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The advantage is that since scattered photons are corrected in the optical path and we attempt to bring all photons emitted from a single spot into a sin- gle detector, we can measure them with a much higher signal-to-noise (SNR) ratio.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' To quantify the quality of a candidate modulation cor- rection, we do not attempt to maximize the total energy emitted from the target.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Rather, we seek to maximize the energy of the corrected wavefront in a single pixel.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We show that despite the fact that we use linear single-photon fluorescence, due to the double correction on both illumi- nation and imaging arms, our score function scales non- linearly with the intensity arriving at the fluorescence tar- get.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Thus, the returning energy at a single pixel is max- imized by a focusing modulation that manages to bring all light into a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We show that effectively, this score function is equivalent to the one used by previous two-photon fluorescence wavefront-shaping work [18].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2 Problem formulation Imaging setup: In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 1 we visualize a wavefront- shaping imaging setup.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A laser beam illuminates a tis- sue sample via a microscope objective.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A phase SLM in the illumination arm modulates the illumination pattern.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We wish to image a fluorescent target at the back of the tissue layer.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The light returning from the target is col- lected via the same objective, and reflected at a dichroic beam-splitter.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A second phase SLM at the imaging arm modulates the emitted light.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Lastly, the modulated light is measured by the front main camera.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In our setup the SLMs (holoeye-pluto) are placed in the Fourier plane of the system.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The setup includes a second validation camera behind the tissue sample to assess focusing quality and image an undistorted reference of the target.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' While earlier research demonstrations of wavefront-shaping use this camera to provide feedback to the algorithm, we emphasize that our goal in this research is to develop non-invasive techniques that can only use feedback by the main (front) camera.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The validation camera cannot provide any input to the algorithm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We note that some research on wavefront shaping and adaptive optics modulates only the illumination or imag- ing arms.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For generality, our problem formulation below will consider modulations at both arms.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Image formation model: Consider a set of K fluores- cent particles inside a sample, and denote their positions by o1, .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' , oK.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We assume the SLM in the illumination arm is illuminated with a spatially uniform plane wave and use the SLM to display a complex 2D electric field that we denote by u.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Although u is a 2D field, we reshape it as a 1D vector.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We also use ν to denote a K ×1 vector of the field propagating through the sample at each of the K fluorescent sources.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The relation between u and ν is linear and can be described as a multiplication by a (very large) matrix ν = T iu.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' T i is the incoming transmission matrix de- scribing coherent light propagation in the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We note that T i is specific to the tissue sample being tested, and 2 Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 1: Our wavefront correction fluorescent microscope setup: A laser beam is exciting fluorescent beads at the back of a tissue layer, and fluorescent emission is scattered again through the tissue, reflects at a dichroic beam-splitter and is collected by a main (front) camera.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We place two SLMs in the Fourier planes of both illumination and imaging arms to allow reshaping these wavefronts.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A validation camera views the beads at the back of the tissue directly.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This camera is not actually used by the algorithm, and is only assessing its success.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' LP=linear polarizer, BS=beam-splitter, DBS=dichroic beam-splitter, BPF=bandpass filter, L1 .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' .' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' L7=lenses, Obj=Objective.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' different tissue samples are described by very different transmission matrices.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For thick tissue T i can be an arbitrarily complex matrix incorporating multiple scat- tering events in the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Likewise, the light returning from the particles to the SLM of the imaging arm can be described as T oν, where T o is the back-propagation transmission matrix.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The propagation of light from the illumination SLM plane to the particles and back to the SLM of the imag- ing arm is then modeled using the combined transmission matrix T a ≡ T o · T i.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (1) We denote by ζ the wavefront placed on the SLM of the imaging arm, and by D(ζ) a diagonal matrix with ζ on its diagonal.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We denote by F the Fourier transform of the wavefront from the SLM plane to the camera sensor plane.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In the fluorescent case, the emissions from different points are incoherent.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The recorded intensity can be ex- pressed as I = � k |FD(ζ)T o ↓,k|2|νk|2α, (2) where |νk|2 is the energy of the excitation light arriving at particle ok, and T o ↓,k is the k-th column of T o, so that FD(ζ)T o ↓,k is the wavefront arriving to the sensor from ok.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Since light emitted from different fluorescent par- ticles changes phase incoherently, effectively the sensor sums the intensity of the wavefronts emitted by differ- ent particles, and their phases do not interfere.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In (2) α denotes the type of fluorescent excitation.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The simplest case α = 1 is known as single-photon fluorescence where the emission is linear in the excitation energy |νk|2.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In two-photon fluorescence, α = 2, namely the emission is proportional to the squared excitation.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Linear fluores- cence is significantly simpler and cheaper to achieve, but as we explain below, a non-linear (two-photon) fluores- cence feedback simplifies modulation estimation.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Phase conjugation: For coherent imaging, the Helmholtz reciprocity principle leads to wave conjuga- tion, namely if we record the wavefront emitted from a source point inside the tissue and play it back in the re- verse direction, the wavefront will focus at the same point.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This implies that the returning transmission matrix is the transpose of the incoming one [25]: T o = T i⊤.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (3) Note that this is just a transpose and not the Hermi- tian (conjugate) transpose.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In the fluorescent case, we should note that T i, T o describe propagation at a dif- ferent wavelength hence they cannot be completely the same.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, for linear single-photon fluorescence the excitation and emission wavelengths are relatively similar and we still assume T o ≈ T i⊤.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Normalization: we assume for simplicity that our trans- mission matrices are normalized such that every column or row has a unit energy, that is for every k � x |T o x,k|2 = 1, � x |T i k,x|2 = 1.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (4) 3 Illumination SLM Validation Arm Imaging Arm Laser Illumination ArmThis means that the total amount of energy that can ar- rive to particle ok or emerge from it is fixed.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As the laser energy is fixed, we also assume w.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='l.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='o.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='g.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' that all illumina- tion vectors have a unit norm ∥u∥ = 1.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As propagation through the tissue does not generate new energy, every incoming vector u should satisfy ∥T iu∥ ≤ 1 and thus the energy at the target is also bounded � k |νk|2 ≤ 1.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (5) 3 Scoring wavefront shaping mod- ulations The first challenge when coming to design a wavefront shaping modulation is coming up with a score function that can actually evaluate the focusing quality facilitated by a candidate modulation mask, using a noninvasive feedback alone.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We start by reviewing scores that were previously introduced in the literature and then propose our new, noise-robust confocal score.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Image quality scores: Modulation evaluation is a sim- pler task when the same modulation can correct a suffi- ciently large isoplanatic image region.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This assumption was made by adaptive optics research [2, 4, 5, 12, 15] and also by wavefront shaping approaches [9,26,36].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' When the same modulation can correct a large image region, one of- ten evaluates the quality of the resulting image, either in terms of contrast [15], sharpness, or variance [36].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' How- ever, for thick tissue, wavefront shaping correction can vary quickly between nearby pixels, and a modulation may only explain a very local region.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This case makes the above image quality scores less applicable, as inher- ently they evaluate the quality of an image region rather then a pixel.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For spatially varying modulations, ideally, we would like to be able to evaluate the success of the modulation based on a per-pixel criteria.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The total intensity score: Consider a configuration where we only try to correct the illumination arm, and the SLM in the imaging arm of Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 1 is not used (equiv- alently, D(ζ) in (2) is the identity matrix).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The easiest score that was considered in the literature [15,18] is just the total intensity measured over the entire sensor plane.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Using (2) and (4) it is easy to show that this total inten- sity score reduces to MTI(u) ≡ � x I(x) = � k |νk|2α.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (6) Since the energy at the target is bounded (see (5)), for the case α > 1 this score is maximized when ν is a one-hot vector, which equals 1 at a single entry and zero at all the others.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Therefore, in two-photon fluorescence finding a good modulation is easy.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' If we manage to modulate the illumination such that it focuses all the excitation energy in a single spot, the emitted power is maximized.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Two-photon fluorescence is however more expensive and harder to implement, and solutions that can use a single-photon excitation feedback are highly desired.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, in the single-photon case where α = 1, (6) re- duces to the total power in ν, MTI(u) = � k |νk|2, and since this power is fixed, the same amount of energy re- turns whether we spread the excitation power over mul- tiple fluorescence sources or bring all of it into one spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Therefore, wavefront shaping using single-photon fluores- cence has remained an open challenge in the literature until recently.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The variance maximization score: Following on a setup that modulates only the illumination and not the imaging arm, Boniface et al.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [3] have recently suggested that to evaluate focusing with linear single-photon feed- back, one should maximize the variance of the intensity measured by the sensor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The idea is that if we manage to focus all the excitation light at a single spot, the emitted light scattered through the tissue will generate a highly varying speckle pattern on the sensor plane.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' If the excita- tion is not focused, multiple sources emit simultaneously.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The light emitted by these sources sums incoherently, and hence the variance of the speckle pattern on the sensor decays.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A short calculation shows MVar(u) ≡ Var[I] ≡ ≡ 1 n � x |I(x)|2 − � 1 n � x I(x) �2 = � k |νk|4, (7) where n is the number of image pixels.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Hence, as before, the score is a non-linear function of the power at differ- ent fluorescent particles and is maximized by a one-hot vector.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This score was an important advance of the state-of- the-art, but it may be hard to evaluate it with suffi- cient noise robustness using weak biological sources.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' To demonstrate this, Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2 visualizes two types of fluores- cent emissions, when excitation light is correctly focused into a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2(a) demonstrates an invitrogen bead (ThermoFisher Fluo-Spheres dark red) that was at- tached to a chicken breast tissue layer.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This is a strong source, and a clear speckle pattern is imaged.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The au- thors of [3] have demonstrated their approach on similar beads.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' However, biological samples are often significantly weaker than such beads.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For example, in Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2(c) we image EGFP neurons sliced out of a mouse brain.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The fluorescent emission here is orders of magnitudes weaker, and the amount of laser power we can apply before the neuron bleaches is also limited.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' One can see that rather than a real speckle pattern, we mostly image noise.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The variance of this image is dominated by the noise variance rather than the actual speckle variance.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 4 (a) scattering, bead (b) focusing, bead (c) scattering, neuron (d) focusing, neuron Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2: Types of fluorescent data: (a,b) emission from invitrogen fluorescent microspheres (excitation/emission at 640/680nm).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A single bead is excited and the emitted light scatters through the tissue to generate a wide speckle pat- tern in (a).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In (b) we use an aberration correction in the imaging arm so that the sensor measures a sharp spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' With such synthetic sources we can image a speckle pattern at high SNR, but this is not always the case with real biological samples.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For example, (c,d) demonstrate fluorescent emission from EGFP neurons (excitation/emission at 490/510nm), which is orders of magnitude weaker.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' When the aberrated wavefront propagates to the sensor a limited number of photons are spread over multiple pixels and noise is dominant.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In (d) we have applied aberration correction in the optics and as all photons are collected by a single pixel, SNR is drastically improved.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Note that images (c,d) are taken under equal exposure and equal excitation power.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Confocal energy score: In this research we suggest a new score for evaluating a wavefront shaping modulation.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' While the previous score corrected only the illumination arm, we suggest to put the same correction at both illu- mination and imaging arms.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The idea is that if we find a modulation focusing all ex- citation light into one spot, due to reciprocity, the same modulation also corrects the emitted light, bringing all of it into a single sensor pixel (assuming the excitation and emission wavelengths are sufficiently similar).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' To score the focusing quality of each modulation we will use the intensity at the central pixel, rather than the total inten- sity throughout the sensor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Assuming the central pixel is measuring the DC compo- nent of the Fourier transformation from the SLM plane to the image plane, the central row of Psens is just a simple averaging.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Thus we can express its value as the product of the SLM modulation (at the imaging arm) with the outgoing transmission matrix: F0,→D(ζ)T o ↓,k = ζT T o ↓,k.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (8) When the same modulation u is used in both illumination and imaging arm, we can express the energy of the central pixel as: MConf(u) ≡ I(0) = = � k |uT T o ↓,k|2|T i k,→u|2 = � k |νk|4.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (9) As before, this score favors one-hot ν vectors and the score is maximized when all light is focused at a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' While this score is equivalent to the variance maxi- mization score above, it is significantly less susceptible to noise.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This is due to the fact that the small number of photons we have at hand are collected by one detector, rather than being spread over multiple pixels.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 2(c- d) shows the images emitted from a single neural spot with and without modulation in the imaging arm, and the significant noise reduction.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In this work we have explicitly optimized the confo- cal score ((9)) using standard Hadamard basis optimiza- tion [23], detailed in the supplement.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This optimization is significantly slower than [1].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As emission is very weak, the fact that the SLM correction is applied before imaging helps collect all photons at one sensor pixel and improve SNR.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Iterative phase conjugation: Recently [1] has pro- posed an incoherent iterative phase conjugation algorithm that can rapidly estimate a wavefront shaping modula- tion.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This algorithm is not explicitly maximizing a cost function.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' It uses fast power iteration to seek an excitation wavefront which is an eigenvector of the transmission ma- trix of the tissue, although the definition of transmission matrices with incoherent light is a bit challenging.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In- tuitively the confocal cost of (9) is maximized when the wavefront T o ↓,k emerging from the system is correlated with the illuminating wavefront u.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This means that the optimum can also be thought of as an eigenvector.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The algorithm of [1] was successfully applied on fluorescent beads, which are both strong and sparse.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In this research we aim to apply the confocal score of (9) to real bio- logical data such as EGFP neurons.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This data is signif- icantly weaker, and also the fluorescent target exhibits a continuous area rather than sparse isolated dots.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The algorithm of [1] heavily relies on the existence of some speckle variation in the input image due to the need to retrieve the phase of the wavefront arriving the sensor from the measured intensity.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Thus, it does not directly apply to continuous fluorescent sources, where not much speckle variation can be measured.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 5 10μm0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='644 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='53 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='416 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='302 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='188 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='07410 μm8.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='264 6.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='649 5.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='034 3.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='419 1.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='804 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='18910gem0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='207 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='171 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='135 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='099 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='063 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='02710 gem1.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='23 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='992 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='753 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='515 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='276 0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='0384 Results We image slices of mice brain with EGFP neurons, ex- cited at 488nm and imaged at 510nm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The mouse brain slices are 50nm thick, so neurons exhibit some 3D varia- tion and modest scattering.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For more challenging scatter- ing we place these slices behind a layer of chicken breast tissue (200−300µm thick) or parafilm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We image fluores- cent emission with a sensitive sCMOS sensor prime BSI express.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3 we visualize some results of our algorithm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Before starting the optimization we focus the objective such that the excitation light observed by the validation camera illuminates the smallest possible area.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(a) shows an image of this excitation pattern from the val- idation camera behind the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As can be observed, the tissue exhibits significant scattering.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We made our best attempts to reduce the diameter of this pattern by adjusting the distance of the objective and the sample, but even at the best focus position, the light scatters to cover a wide sample area.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(b) we visualize the excitation light after optimizing the wavefront shaping modulation, which is nicely focused into a sharp spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(c-d) we have placed a band-pass filter on the val- idation camera to show the emission light.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Before opti- mization a wide area is excited and we can see the neuron shape.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' At the end of the optimization a single point is excited.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(e-f) we visualize the views of the front main camera, providing the sole input our algorithm can access.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Before optimization the emitted light is scattered over a wide sensor area.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As a low number of photons is spread over multiple sensor pixels, the captured imaged is very noisy.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Despite this low SNR, at the end of the optimization the aberration is corrected and all the pho- tons are brought into a single sensor pixel, leading to a high quality image where noise is much less visible, see Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(f).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3(g) we demonstrate the actual point spread function of the tissue aberration.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For that we have used the correction only at the illumination arm and fo- cused the illumination to excite a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We used a blank SLM at the imaging arm so the emitted light is not corrected.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' One can see that the aberration of a single flu- orescent target is not negligible.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We emphasize that each of the images in Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3 is normalized so that its maximum is 1, but clearly the spot at the focused images received a much higher number of photons than the wide scattering images of unfocused light, despite the fact that all images were captured under equal exposure and equal excitation power.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 4 we use the recovered wavefront shaping mod- ulation to image a wide area rather than a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' For that we excite a wide area and use a correction only at the imaging arm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Due to the memory effect [17, 22], the same modulation can allow us to image a small lo- cal patch rather than a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' With the correction, the neuron is observed with a much higher contrast and even the axons (thin lines around the neuron) emerging from it, whose emission is much weaker, can be partially observed.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' As our SLMs are placed in the Fourier plane of the system and not at a plane conjugate to the sam- ple itself as suggested by [21], we tilt-shift the modulated pattern to image a somewhat wider area, as explained in [1].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 5 Discussion In this research we have analyzed score functions for wave- front shaping correction using non-invasive feedback at the absence of a guiding star.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Obtaining such feedback is challenging, because even if excitation light is corrected and focused at a single object spot, the light returning to the sensor is undergoing another aberration process while propagating through the tissue, leading to yet another scattered pattern.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Moreover, real biological fluorescent sources are weak emitting a limited number of photons.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' When these photons are spread over multiple sensor pix- els the detectable signal is highly contaminated by noise.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' To assess focusing quality, we need a score function that can measure a non-linear function of the light emitted by different sources.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' This is naturally achieved when using two-photon fluorescent feedback, but is harder to achieve with linear fluorescence.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We show that by using a confo- cal correction at both illumination and imaging arms we can measure such a non-linear feedback, which is maxi- mized when all excitation light is brought into one spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Moreover, the fact that our system uses a correction of the emitted light as part of the optical path allows us to bring the limited number of emitted photons into a single sensor spot, facilitating a high SNR measurement.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' The drawback of our current approach is that it uses a slow Hadamard basis optimization [23].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In our cur- rent implementation it takes about 30 min to optimize for one modulation pattern.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Some of this can be largely optimized by better hardware such as a faster SLM.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' How- ever, due to the large number of iterations required by the simple coordinate descent optimization, this approach is inherently slower than the power iterations of [1].' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We are exploring ways to accelerate our current optimization by extending the phase retrieval framework of [1] to model the full image formation model of the incoherent case.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' References [1] Aizik, D.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Gkioulekas, I.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', and Levin, A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Fluo- rescent wavefront shaping using incoherent iterative phase conjugation.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Optica 9, 7 (Jul 2022), 746–754.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 6 (a) Valid.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' laser (b) Valid.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' laser (c) Valid.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' fluor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (d) Valid.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' fluor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (e) Main fluor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (f) Main fluor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (g) Main fluor.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' No modulation With modulation No modulation With modulation No modulation With modulation Point aberration Fig.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3: Wavefront shaping results: we visualize views from the validation and main cameras, at the beginning of the algorithm where no correction is applied, compared to the modulated image at the end of the optimization.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (a-b) The excitation light as viewed by the validation camera at the back of the tissue.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Due to significant scattering, at the beginning a wide speckle pattern is generated, but after optimization, the modulated wavefront is brought into a single spot.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (c-d) By placing a band-pass filter on the validation camera we visualize the emitted light with and without correction.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (e-f) Views of the emitted light at the main front camera with and without correction.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Note that this is the only input used by our algorithm.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Without correction, light is scattered over a wide image area and is being measured with a very low SNR.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A sharp clean spot can be imaged when the limited number of photons is corrected in the optical path and brought into a single sensor pixel.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' (g) By correcting the emission such that a single spot is excited and leaving the imaging path uncorrected, we can visualize the actual aberration of a single fluorescent point source.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [2] Antonello, J.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Barbotin, A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Chong, E.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Z.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Rittscher, J.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', and Booth, M.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' J.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Multi-scale sensorless adaptive optics: application to stimulated emission depletion microscopy.' metadata={'source': 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'/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Noninvasive light focusing in scattering media using speckle variance optimization.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Optica (2019).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [4] Bonora, S.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', and Zawadzki, R.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' J.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Wavefront sen- sorless modal deformable mirror correction in adap- tive optics: 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2014), e165.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [6] Booth, M.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' J.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Neil, M.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Juˇskaitis, R.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', 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metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Veeraraghavan, A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', and Sankaranarayanan, A.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' C.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 3PointTM: Faster measurement of high- dimensional transmission matrices.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' In Euro.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Conf.' metadata={'source': 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metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', and Cui, M.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Complex wave- front corrections for deep tissue focusing using low coherence backscattered light.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Opt.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Express 20, 15 (Jul 2012), 16532–16543.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [11] Gigan, S.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Katz, O.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', et al.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Roadmap on wave- front shaping and deep imaging in complex media.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' arXiv preprint arXiv:2111.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='14908 (2021).' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' 7 10μm10 μm10 μm10μm10μm0.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content='176 0.' metadata={'source': 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'/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' We compare this to an undistorted reference viewed by the validation camera, and to the initial uncorrected image of the main camera.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' Notice how the neuron contrast is improved and even some of the axons are revealed.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=' [12] Hampson, K.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Turcotte, R.' metadata={'source': '/home/zjlab/wf/langchain-ChatGLM/knowledge_base/CtFJT4oBgHgl3EQfAiym/content/2301.11421v1.pdf'} +page_content=', Miller, D.' metadata={'source': 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