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27 Janelia Publications

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    09/03/21 | Deep learning enables fast and dense single-molecule localization with high accuracy
    Speiser A, Müller L, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC
    Nature Methods. 2021 Sep 03;18(9):. doi: 10.1101/2020.10.26.355164

    Single-molecule localization microscopy (SMLM) has had remarkable success in imaging cellular structures with nanometer resolution, but the need for activating only single isolated emitters limits imaging speed and labeling density. Here, we overcome this major limitation using deep learning. We developed DECODE, a computational tool that can localize single emitters at high density in 3D with highest accuracy for a large range of imaging modalities and conditions. In a public software benchmark competition, it outperformed all other fitters on 12 out of 12 data-sets when comparing both detection accuracy and localization error, often by a substantial margin. DECODE allowed us to take live-cell SMLM data with reduced light exposure in just 3 seconds and to image microtubules at ultra-high labeling density. Packaged for simple installation and use, DECODE will enable many labs to reduce imaging times and increase localization density in SMLM.Competing Interest StatementThe authors have declared no competing interest.

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    07/01/21 | Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset
    Buhmann J, Sheridan A, Gerhard S, Krause R, Nguyen T, Heinrich L, Schlegel P, Lee WA, Wilson R, Saalfeld S, Jefferis G, Bock D, Turaga S, Cook M, Funke J
    Nature Methods. 2021 Jul 1;18(7):771-4. doi: 10.1038/s41592-021-01183-7

    The study of neural circuits requires the reconstruction of neurons and the identification of synaptic connections between them. To scale the reconstruction to the size of whole-brain datasets, semi-automatic methods are needed to solve those tasks. Here, we present an automatic method for synaptic partner identification in insect brains, which uses convolutional neural networks to identify post-synaptic sites and their pre-synaptic partners. The networks can be trained from human generated point annotations alone and requires only simple post-processing to obtain final predictions. We used our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) electron microscopy (EM) dataset and evaluated its accuracy on 146,643 synapses from 702 neurons with a total cable length of 312 mm in four different brain regions. The predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy: 96% of edges between connected neurons are correctly classified as weakly connected (less than five synapses) and strongly connected (at least five synapses). Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons.

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    04/21/21 | Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
    Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Rogerson LE, Sofroniew NJ, Reimer J, Froudarakis E, Euler T, Román Rosón M, Theis L, Tolias AS, Bethge M, Bush D
    PLOS Computational Biology. Sep-05-2019;14(5):e1006157. doi: 10.1371/journal.pcbi.1006157

    In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

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    01/01/20 | Comparative single-cell transcriptomics of complete insect nervous systems
    Cocanougher BT, Wittenbach JD, Long XS, Kohn AB, Norekian TP, Yan J, Colonell J, Masson J, Truman JW, Cardona A, Turaga SC, Singer RH, Moroz LL, Zlatic M
    bioRxiv. 01/2020:. doi: 10.1101/785931

    Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits, and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval central nervous system composed of over 200,000 single cells across four developmental stages. We develop polyseq, a python package, to perform cell-type analyses. We use single-molecule RNA-FISH to validate our scRNAseq findings. To investigate how internal state affects cell state, we optogentically altered internal state with high-throughput behavior protocols designed to mimic wasp sting and over activation of the memory system. We found nervous system-wide and neuron-specific gene expression changes. This resource is valuable for developmental biology and neuroscience, and it advances our understanding of how genes, neurons, and circuits generate behavior.

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    10/24/19 | Importance Weighted Adversarial Variational Autoencoders for Spike Inference from Calcium Imaging Data
    Daniel Jiwoong Im , Sridhama Prakhya , Jinyao Yan , Srinivas C. Turaga , Kristin Branson
    CoRR. 10/2019;abs/1906.03214:

    The Importance Weighted Auto Encoder (IWAE) objective has been shown to improve the training of generative models over the standard Variational Auto Encoder (VAE) objective. Here, we derive importance weighted extensions to Adversarial Variational Bayes (AVB) and Adversarial Autoencoder (AAE). These latent variable models use implicitly defined inference networks whose approximate posterior density qφ(z|x) cannot be directly evaluated, an essential ingredient for importance weighting. We show improved training and inference in latent variable models with our adversarially trained importance weighting method, and derive new theoretical connections between adversarial generative model training criteria and marginal likelihood based methods. We apply these methods to the important problem of inferring spiking neural activity from calcium imaging data, a challenging posterior inference problem in neuroscience, and show that posterior samples from the adversarial methods outperform factorized posteriors used in VAEs.

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    10/04/20 | Learning Guided Electron Microscopy with Active Acquisition
    Mi L, Wang H, Meirovitch Y, Schalek R, Turaga SC, Lichtman JW, Samuel AD, Shavit N, Martel AL, Abolmaesumi P, Stoyanov D, Mateus D, Zuluaga MA, Zhou SK, Racoceanu D, Joskowicz L
    Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. 10/2020:

    Single-beam scanning electron microscopes (SEM) are widely used to acquire massive datasets for biomedical study, material analysis, and fabrication inspection. Datasets are typically acquired with uniform acquisition: applying the electron beam with the same power and duration to all image pixels, even if there is great variety in the pixels' importance for eventual use. Many SEMs are now able to move the beam to any pixel in the field of view without delay, enabling them, in principle, to invest their time budget more effectively with non-uniform imaging.

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    01/01/21 | Local Shape Descriptors for Neuron Segmentation
    Sheridan A, Nguyen T, Deb D, Lee WA, Saalfeld S, Turaga S, Manor U, Funke J
    bioRxiv. 2021/01:. doi: 10.1101/2021.01.18.427039

    We present a simple, yet effective, auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of Local Shape Descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors are designed to capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a large study comparing several existing methods across various specimen, imaging techniques, and resolutions, we find that auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinitybased segmentation methods to be on par with the current state of the art for neuron segmentation (Flood-Filling Networks, FFN), while being two orders of magnitudes more efficient—a critical requirement for the processing of future petabyte-sized datasets. Implementations of the new auxiliary learning task, network architectures, training, prediction, and evaluation code, as well as the datasets used in this study are publicly available as a benchmark for future method contributions.Competing Interest StatementThe authors have declared no competing interest.

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    04/21/21 | Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit
    Aitchison L, Russell L, Packer AM, Yan J, Castonguay P, Häusser M, Turaga SC, I. Guyon , U. V. Luxburg , S. Bengio , H. Wallach , R. Fergus , S. Vishwanathan , R. Garnett
    Advances in Neural Information Processing Systems:

    Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons. Additionally, we model two properties of the optogenetic perturbation: off-target photostimulation and photostimulation transients. Using this model, we were able to fit models on 30 minutes of data in just 10 minutes. We performed an all-optical circuit mapping experiment in primary visual cortex of the awake mouse, and use our approach to predict neural connectivity between excitatory neurons in layer 2/3. Predicted connectivity is sparse and consistent with known correlations with stimulus tuning, spontaneous correlation and distance.



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    03/26/21 | SongExplorer: A deep learning workflow for discovery and segmentation of animal acoustic communication signals
    Arthur BJ, Ding Y, Sosale M, Khalif F, Kim E, Waddell P, Turaga SC, Stern DL
    bioRxiv. 03/2021:. doi: 10.1101/2021.03.26.437280

    Many animals produce distinct sounds or substrate-borne vibrations, but these signals have proved challenging to segment with automated algorithms. We have developed SongExplorer, a web-browser based interface wrapped around a deep-learning algorithm that supports an interactive workflow for (1) discovery of animal sounds, (2) manual annotation, (3) supervised training of a deep convolutional neural network, and (4) automated segmentation of recordings. Raw data can be explored by simultaneously examining song events, both individually and in the context of the entire recording, watching synced video, and listening to song. We provide a simple way to visualize many song events from large datasets within an interactive low-dimensional visualization, which facilitates detection and correction of incorrectly labelled song events. The machine learning model we implemented displays higher accuracy than existing heuristic algorithms and similar accuracy as two expert human annotators. We show that SongExplorer allows rapid detection of all song types from new species and of novel song types in previously well-studied species.Competing Interest StatementThe authors have declared no competing interest.

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    06/27/19 | Teaching deep neural networks to localize single molecules for super-resolution microscopy
    Speiser A, Müller L, Matti U, Obara CJ, Legant WR, Ries J, Macke JH, Turaga SC
    arXiv e-prints. 06/2019:arXiv:1907.00770

    Single-molecule localization fluorescence microscopy constructs super-resolution images by sequential imaging and computational localization of sparsely activated fluorophores. Accurate and efficient fluorophore localization algorithms are key to the success of this computational microscopy method. We present a novel localization algorithm based on deep learning which significantly improves upon the state of the art. Our contributions are a novel network architecture for simultaneous detection and localization, and new loss function which phrases detection and localization as a Bayesian inference problem, and thus allows the network to provide uncertainty-estimates. In contrast to standard methods which independently process imaging frames, our network architecture uses temporal context from multiple sequentially imaged frames to detect and localize molecules. We demonstrate the power of our method across a variety of datasets, imaging modalities, signal to noise ratios, and fluorophore densities. While existing localization algorithms can achieve optimal localization accuracy at low fluorophore densities, they are confounded by high densities. Our method is the first deep-learning based approach which achieves state-of-the-art on the SMLM2016 challenge. It achieves the best scores on 12 out of 12 data-sets when comparing both detection accuracy and precision, and excels at high densities. Finally, we investigate how unsupervised learning can be used to make the network robust against mismatch between simulated and real data. The lessons learned here are more generally relevant for the training of deep networks to solve challenging Bayesian inverse problems on spatially extended domains in biology and physics.

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