@article {69902, title = {Chromatix: a differentiable, GPU-accelerated wave-optics library}, journal = {bioRxiv}, year = {2025}, month = {2025 May 2}, abstract = {

Modern microscopy methods incorporate computational modeling of optical systems as an integral part of the imaging process, either to solve inverse problems or enable optimization of the optical system design. These methods often depend on differentiable simulations of optical systems, yet no standardized framework exists{\textemdash}forcing computational optics researchers to repeatedly and independently implement simulations that are prone to errors, difficult to reuse in other applications, and often computationally suboptimal. These common problems limit the potential impact of computational optics as a field. We present Chromatix: an open-source, GPU-accelerated differentiable wave optics library. Chromatix builds on JAX to enable fast simulation of diverse optical systems and inverse problem solving, scaling these simulations from single-CPU laptops to multi-GPU servers. The library implements various optical elements (e.g., lenses, polarizers and spatial light modulators) and multiple light propagation models (e.g., Fresnel approximation, angular spectrum and off-axis propagation) that can be flexibly combined to model various computational optics applications such as snapshot microscopy, holography, and phase retrieval of multiple scattering samples. These simulations can be automatically parallelized to scale across multiple GPUs with a single-line change to the modeling code, enabling simulation and optimization of previously impractical optical system designs. We demonstrate Chromatix{\textquoteright}s capacity to substantially accelerate optics simulation and optimization on existing methods in computational optics, speeding up optical simulation and optimization from 2-6{\texttimes} on a single GPU to up to 22{\texttimes} on 8 GPUs (depending on the particular system being modeled) compared to the original implementations. Chromatix establishes a standard for wave optics simulations, democratizing access to and expanding the design space of computational optics.i

}, doi = {10.1101/2025.04.29.651152}, url = {https://www.biorxiv.org/content/early/2025/05/02/2025.04.29.651152}, author = {Deb, Diptodip and Both, Gert-Jan and Bezzam, Eric and Kohli, Amit and Yang, Siqi and Chaware, Amey and Allier, C{\'e}dric and Cai, Changjia and Anderberg, Geneva and Eybposh, M. Hossein and Schneider, Magdalena C. and Heintzmann, Rainer and Rivera-Sanchez, Fabrizio A. and Simmerer, Corey and Meng, Guanghan and Tormes-Vaquerano, Jovan and Han, SeungYun and Shanmugavel, Sibi Chakravarthy and Maruvada, Teja and Yang, Xi and Kim, Yewon and Diederich, Benedict and Joo, Chulmin and Waller, Laura and Durr, Nicholas J. and P{\'e}gard, Nicolas C. and La Rivi{\`e}re, Patrick J. and Horstmeyer, Roarke and Chowdhury, Shwetadwip and Turaga, Srinivas C.} } @article {65321, title = {Rapid mesoscale volumetric imaging of neural activity with synaptic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {291-4}, abstract = {

Imaging neurons and neural circuits over large volumes at high speed and subcellular resolution is a difficult task. Incorporating a Bessel focus module into a two-photon fluorescence mesoscope, we achieved rapid volumetric imaging of neural activity over the mesoscale with synaptic resolution. We applied the technology to calcium imaging of entire dendritic spans of neurons as well as neural ensembles within multiple cortical regions over two hemispheres of the awake mouse brain.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0760-9}, author = {Lu, Rongwen and Liang, Yajie and Meng, Guanghan and Zhou, Pengcheng and Svoboda, Karel and Paninski, Liam and Ji, Na} } @article {49597, title = {High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging .}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 03}, abstract = {

Optical imaging has become a powerful tool for studying brains . The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus .

}, issn = {2050-084X}, doi = {10.7554/eLife.40805}, author = {Meng, Guanghan and Liang, Yajie and Sarsfield, Sarah and Jiang, Wan-Chen and Lu, Rongwen and Dudman, Joshua Tate and Aponte, Yeka and Ji, Na} } @article {49367, title = {In vivo measurement of afferent activity with axon-specific calcium imaging.}, journal = {Nature Neuroscience}, year = {2018}, month = {2018 Aug 20}, abstract = {

In vivo calcium imaging from axons provides direct interrogation of afferent neural activity, informing the neural representations that a local circuit receives. Unlike in somata and dendrites, axonal recording of neural activity-both electrically and optically-has been difficult to achieve, thus preventing comprehensive understanding of neuronal circuit function. Here we developed an active transportation strategy to enrich GCaMP6, a genetically encoded calcium indicator, uniformly in axons with sufficient brightness, signal-to-noise ratio, and photostability to allow robust, structure-specific imaging of presynaptic activity in awake mice. Axon-targeted GCaMP6 enables frame-to-frame correlation for motion correction in axons and permits subcellular-resolution recording of axonal activity in previously inaccessible deep-brain areas. We used axon-targeted GCaMP6 to record layer-specific local afferents without contamination from somata or from intermingled dendrites in the cortex. We expect that axon-targeted GCaMP6 will facilitate new applications in investigating afferent signals relayed by genetically defined neuronal populations within and across specific brain regions.

}, issn = {1546-1726}, doi = {10.1038/s41593-018-0211-4}, author = {Broussard, Gerard Joey and Liang, Yajie and Fridman, Marina and Unger, Elizabeth K and Meng, Guanghan and Xiao, Xian and Ji, Na and Petreanu, Leopoldo and Tian, Lin} }