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5017 Results

Showing 4641-4650 of 5017 results
Lab
Tillberg Lab
Our lab has an initial priority of further developing and applying Expansion Microscopy, particularly in a complementary role with vivo circuit characterization of the same specimen.
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People
Tim Brown
Scientific Operations Director - Biology
People
Tim Harris
Senior Fellow
People
Tim Wang
Visiting Scientist
Publications
12/17/25 | Time or distance encoding by hippocampal neurons via heterogeneous ramping rates.
Heldman R, Pang D, Zhao X, Mensh B, Wang Y
Nat Commun. 2025 Dec 17;16(1):11083. doi: 10.1038/s41467-025-67038-3

To navigate their environments effectively, animals frequently track time elapsed or distance traveled while seeking food and avoiding threats. The hippocampus is implicated in this process, but the neural mechanisms remain unclear. Using virtual reality tasks that require mice to integrate time or distance to collect a reward, we identified two previously unknown functional subpopulations of CA1 pyramidal neurons. Both subpopulations encode time or distance via distinct ramping dynamics. The first subpopulation exhibits a rapid, synchronous rise in activity upon movement-initiated integration. Subsequently, individual neurons ramp down at heterogeneous rates, creating progressively diverging firing rates that encode elapsed time or distance. Closed-loop optogenetic inactivation of somatostatin-positive (SST) interneurons counterintuitively reduced the ramping activity, leading mice to prematurely attempt reward collection, suggesting impaired time/distance estimation. Conversely, the second CA1 subpopulation shows opposite dynamics - an initial rapid suppression followed by a gradual ramp-up. Inactivating parvalbumin-positive (PV) interneurons diminished this initial suppression, resulting in transient attempts to collect reward near integration onset. These findings reveal parallel hippocampal circuits that initiate and maintain time or distance encoding, controlled by PV and SST interneurons, respectively, and provide insights into the neural computations supporting goal-directed navigation.

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Publications
04/01/17 | Time-accuracy tradeoffs in kernel prediction: controlling prediction quality.
Kpotufe S, Verma N
Journal of Machine Learning Research. 2017 Apr 1 ;18(44):1-29

Kernel regression or classification (also referred to as weighted ε-NN methods in Machine Learning) are appealing for their simplicity and therefore ubiquitous in data analysis. How- ever, practical implementations of kernel regression or classification consist of quantizing or sub-sampling data for improving time efficiency, often at the cost of prediction quality. While such tradeoffs are necessary in practice, their statistical implications are generally not well understood, hence practical implementations come with few performance guaran- tees. In particular, it is unclear whether it is possible to maintain the statistical accuracy of kernel prediction—crucial in some applications—while improving prediction time.

The present work provides guiding principles for combining kernel prediction with data- quantization so as to guarantee good tradeoffs between prediction time and accuracy, and in particular so as to approximately maintain the good accuracy of vanilla kernel prediction.

Furthermore, our tradeoff guarantees are worked out explicitly in terms of a tuning parameter which acts as a knob that favors either time or accuracy depending on practical needs. On one end of the knob, prediction time is of the same order as that of single-nearest- neighbor prediction (which is statistically inconsistent) while maintaining consistency; on the other end of the knob, the prediction risk is nearly minimax-optimal (in terms of the original data size) while still reducing time complexity. The analysis thus reveals the interaction between the data-quantization approach and the kernel prediction method, and most importantly gives explicit control of the tradeoff to the practitioner rather than fixing the tradeoff in advance or leaving it opaque.

The theoretical results are validated on data from a range of real-world application domains; in particular we demonstrate that the theoretical knob performs as expected. 

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Publications
08/23/25 | Time-deterministic cryo-optical microscopy.
Tsuji K, Yamanaka M, Kumamoto Y, Tamura S, Miyamura W, Kubo T, Mizushima K, Kono K, Hirano H, Shiozaki M, Zhao X, Xi H, Sugiura K, Fukushima S, Kunimoto T, Tanabe Y, Nishida K, Mochizuki K, Harada Y, Smith NI, Heintzmann R, Yu Z, Wang MC, Nagai T, Tanaka H, Fujita K
Light Sci Appl. 2025 Aug 23;14(1):275. doi: 10.1038/s41377-025-01941-8

Fluorescence microscopy enables the visualization of cellular morphology, molecular distribution, ion distribution, and their dynamic behaviors during biological processes. Enhancing the signal-to-noise ratio (SNR) in fluorescence imaging improves the quantification accuracy and spatial resolution; however, achieving high SNR at fast image acquisition rates, which is often required to observe cellular dynamics, still remains a challenge. In this study, we developed a technique to rapidly freeze biological cells in milliseconds during optical microscopy observation. Compared to chemical fixation, rapid freezing provides rapid immobilization of samples while more effectively preserving the morphology and conditions of cells. This technique combines the advantages of both live-cell and cryofixation microscopy, i.e., temporal dynamics and high SNR snapshots of selected moments, and is demonstrated by fluorescence and Raman microscopy with high spatial resolution and quantification under low temperature conditions. Furthermore, we also demonstrated that intracellular calcium dynamics can be frozen rapidly and visualized using fluorescent ion indicators, suggesting that ion distribution and conformation of the probe molecules can be fixed both spatially and temporally. These results confirmed that our technique can time-deterministically suspend and visualize cellular dynamics while preserving molecular and ionic states, indicating the potential to provide detailed insights into sample dynamics with improved spatial resolution and temporal accuracy in observations.

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Publications
04/03/12 | Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination.
Fiolka R, Shao L, Rego EH, Davidson MW, Gustafsson MG
Proceedings of the National Academy of Sciences of the United States of America. 2012 Apr 3;109(14):5311-5. doi: 10.1073/pnas.1119262109

Previous implementations of structured-illumination microscopy (SIM) were slow or designed for one-color excitation, sacrificing two unique and extremely beneficial aspects of light microscopy: live-cell imaging in multiple colors. This is especially unfortunate because, among the resolution-extending techniques, SIM is an attractive choice for live-cell imaging; it requires no special fluorophores or high light intensities to achieve twice diffraction-limited resolution in three dimensions. Furthermore, its wide-field nature makes it light-efficient and decouples the acquisition speed from the size of the lateral field of view, meaning that high frame rates over large volumes are possible. Here, we report a previously undescribed SIM setup that is fast enough to record 3D two-color datasets of living whole cells. Using rapidly programmable liquid crystal devices and a flexible 2D grid pattern algorithm to switch between excitation wavelengths quickly, we show volume rates as high as 4 s in one color and 8.5 s in two colors over tens of time points. To demonstrate the capabilities of our microscope, we image a variety of biological structures, including mitochondria, clathrin-coated vesicles, and the actin cytoskeleton, in either HeLa cells or cultured neurons.

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Publications
03/24/23 | Time-resolved correlation of distributed brain activity tracks E-I balance and accounts for diverse scale-free phenomena.
Nanda A, Johnson GW, Mu Y, Ahrens MB, Chang C, Englot DJ, Breakspear M, Rubinov M
Cell Reports. 2023 Mar 24;42(4):112254. doi: 10.1016/j.celrep.2023.112254

Much of systems neuroscience posits the functional importance of brain activity patterns that lack natural scales of sizes, durations, or frequencies. The field has developed prominent, and sometimes competing, explanations for the nature of this scale-free activity. Here, we reconcile these explanations across species and modalities. First, we link estimates of excitation-inhibition (E-I) balance with time-resolved correlation of distributed brain activity. Second, we develop an unbiased method for sampling time series constrained by this time-resolved correlation. Third, we use this method to show that estimates of E-I balance account for diverse scale-free phenomena without need to attribute additional function or importance to these phenomena. Collectively, our results simplify existing explanations of scale-free brain activity and provide stringent tests on future theories that seek to transcend these explanations.

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