Biology subjects

Mackevicius, E. L.

Publications and source records attributed to Mackevicius, E. L..

6 recordsLinked to original sources

bioRxiv2025

Computational Urban Ecology of New York City Rats

Urban rats are highly adaptable, thriving in the dynamic and often inhospitable conditions of modern cities. Despite substantial mitigation efforts, they remain an enduring presence in urban environments, yet surprisingly little is known about the daily lives and behavioral strategies that underlie their success. Here, we conducted fieldwork on free-ranging rats in New York City, using thermal imaging and ultrasonic audio recordings. We apply cutting-edge artificial intelligence techniques to capture high-resolution movement patterns and generate 3D reconstructions of foraging environments including subways, streets, and parks. We characterize social vocalizations across environmental contexts, and compare the patterns of social communication observed in NYC rats to the distribution of rodent vocalizations reported in the literature. This work provides a foundation for translating techniques and theories of rodent cognition from the lab to urban ecological settings.

animal behavior and cognition↗

bioRxiv2023

Barcoding of episodic memories in the hippocampus of a food-caching bird

Episodic memory, or memory of experienced events, is a critical function of the hippocampus1-3. It is therefore important to understand how hippocampal activity represents specific events in an animals life. We addressed this question in chickadees - specialist food-caching birds that hide food at scattered locations and use memory to find their caches later in time4, 5. We performed high-density neural recordings in the hippocampus of chickadees as they cached and retrieved seeds in a laboratory arena. We found that each caching event was represented by a burst of firing in a unique set of hippocampal neurons. These barcode-like patterns of activity were sparse (<10% of neurons active), uncorrelated even for immediately adjacent caches, and different even for separate caches at the same location. The barcode representing a specific caching event was transiently reactivated whenever a bird later interacted with the same cache - for example, to retrieve food. Barcodes co-occurred with conventional place cell activity6, 7, as well as location-independent responses to cached seeds. We propose that barcodes are signatures of episodic memories evoked during memory recall. These patterns assign a unique identifier to each event and may be a mechanism for rapid formation and storage of many non-interfering memories.

neuroscience↗

bioRxiv2023

Spatial Tracking Across Time (ST AT ): Tracking Neurons Across In-Vivo Imaging Sessions through Optimizing Local Neighborhood Motion Consistency

Chronic calcium imaging has become a powerful and indispensable tool for analyzing the long-term stability and plasticity of neuronal activity. One crucial step of the data processing pipeline is to register individual neurons across imaging sessions, which usually extend over a few days or even months, and show various levels of spatial deformation of the imaged field of view (FOV). Previous solutions align FOVs of all sessions first and then register the same neurons according to their shapes and locations [1, 2]. However, the FOV registration is computational intensive, especially in the case of nonrigid case. Here we propose a cell tracking method that does not require FOV image registration. Specifically, the algorithm STAT (short for Stay T ogether, Align Together, and for Spatial Tracking Across Time) represents neurons from two sessions as two sets of neuronal centroids, uses point set registration (PSR) to find a spatially smooth transformation to align them while assigning correspondences. The optimization method iteratively updates between the general motion and individual neuron identity tracking, an idea seen in the computer vision literatures [3, 4]. Our method can be thought of as a specialization and simplification of these more general methods to calcium imaging neuron tracking. We validate STAT on datasets with simulated nonrigid motion that is hard to motion correct without extensive manual intervention. Next, we test STAT on experimental data from singing birds collected on three different days, and observe stable song-locked activity across days. An example use case of this package is reference [5].

neuroscience↗

bioRxiv2023

An entorhinal-like region in food-caching birds

The mammalian entorhinal cortex routes inputs from diverse sources into the hippocampus. This information is mixed and expressed in the activity of many specialized entorhinal cell types, which are considered indispensable for hippocampal function. However, functionally similar hippocampi exist even in non-mammals that lack an obvious entorhinal cortex, or generally any layered cortex. To address this dilemma, we mapped extrinsic hippocampal connections in chickadees, whose hippocampi are used for remembering numerous food caches. We found a well-delineated structure in these birds that is topologically similar to the entorhinal cortex and interfaces between the hippocampus and other pallial regions. Recordings of this structure revealed entorhinal-like activity, including border and multi-field grid-like cells. These cells were localized to the subregion predicted by anatomical mapping to match the dorsomedial entorhinal cortex. Our findings uncover an anatomical and physiological equivalence of vastly different brains, suggesting a fundamental nature of entorhinal-like computations for hippocampal function.

neuroscience↗

bioRxiv2022

Self-organization of songbird neural sequences during social isolation

Behaviors emerge via a combination of experience and innate predis-positions. As the brain matures, it undergoes major changes in cellular, network and functional properties that can be due to sensory experience as well as developmental processes. In normal birdsong learning, neural sequences emerge to control song syllables learned from a tutor. Here, we disambiguate the role of experience and development in neural sequence formation by delaying exposure to a tutor. Using functional calcium imaging, we observe neural sequences in the absence of tutoring, demonstrating that experience is not necessary for the formation of sequences. However, after exposure to a tutor, pre-existing sequences can become tightly associated with new song syllables. Since we delayed tutoring, only half our birds learned new syllables following tutor exposure. The birds that failed to learn were the birds in which pre-tutoring neural sequences were most crystallized, that is, already tightly associated with their (untutored) song.

neuroscience↗

bioRxiv2018

Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience

Identifying low-dimensional features that describe large-scale neural recordings is a major challenge in neuroscience. Repeated temporal patterns (sequences) are thought to be a salient feature of neural dynamics, but are not succinctly captured by traditional dimensionality reduction techniques. Here we describe a software toolbox--called seqNMF--with new methods for extracting informative, non-redundant, sequences from high-dimensional neural data, testing the significance of these extracted patterns, and assessing the prevalence of sequential structure in data. We test these methods on simulated data under multiple noise conditions, and on several real neural and behavioral data sets. In hippocampal data, seqNMF identifies neural sequences that match those calculated manually by reference to behavioral events. In songbird data, seqNMF discovers neural sequences in untutored birds that lack stereotyped songs. Thus, by identifying temporal structure directly from neural data, seqNMF enables dissection of complex neural circuits without relying on temporal references from stimuli or behavioral outputs.

neuroscience↗