Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Ca2+ is a highly versatile intracellular signal that operates over a wide temporal range to regulate many different cellular processes. An extensive Ca2+-signalling toolkit is used to assemble signalling systems with very different spatial and temporal dynamics. Rapid highly localized Ca2+ spikes regulate fast responses, whereas slower responses are controlled by repetitive global Ca2+ transients or intracellular Ca2+ waves. Ca2+ has a direct role in controlling the expression patterns of its signalling systems that are constantly being remodelled in both health and disease.

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Calcium signalling: dynamics, homeostasis and remodelling

With few exceptions biological tissues strongly scatter light, making high-resolution deep imaging impossible for traditional⎯including confocal⎯fluorescence microscopy. Nonlinear optical microscopy, in particular two photon–excited fluorescence microscopy, has overcome this limitation, providing large depth penetration mainly because even multiply scattered signal photons can be assigned to their origin as the result of localized nonlinear signal generation. Two-photon microscopy thus allows cellular imaging several hundred microns deep in various organs of living animals. Here we review fundamental concepts of nonlinear microscopy and discuss conditions relevant for achieving large imaging depths in intact tissue.

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Deep tissue two-photon microscopy

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Principles Of Optics Electromagnetic Theory Of Propagation Interference And Diffraction Of Light

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.

/pdf/imaging-neural-activity-in-worms-flies-and-mice-with-3p3ty3yt7l.pdf

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

In the vertebrate visual system, all output of the retina is carried by retinal ganglion cells. Each type encodes distinct visual features in parallel for transmission to the brain. How many such 'output channels' exist and what each encodes are areas of intense debate. In the mouse, anatomical estimates range from 15 to 20 channels, and only a handful are functionally understood. By combining two-photon calcium imaging to obtain dense retinal recordings and unsupervised clustering of the resulting sample of more than 11,000 cells, here we show that the mouse retina harbours substantially more than 30 functional output channels. These include all known and several new ganglion cell types, as verified by genetic and anatomical criteria. Therefore, information channels from the mouse eye to the mouse brain are considerably more diverse than shown thus far by anatomical studies, suggesting an encoding strategy resembling that used in state-of-the-art artificial vision systems.

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The functional diversity of retinal ganglion cells in the mouse

The detection of image motion is fundamental to vision. In many species, unique classes of retinal ganglion cells selectively respond to visual stimuli that move in specific directions. It is not known which retinal cell first performs the neural computations that give rise to directional selectivity in the ganglion cell. A prominent candidate has been an interneuron called the 'starburst amacrine cell'. Using two-photon optical recordings of intracellular calcium concentration, here we find that individual dendritic branches of starburst cells act as independent computation modules. Dendritic calcium signals, but not somatic membrane voltage, are directionally selective for stimuli that move centrifugally from the cell soma. This demonstrates that direction selectivity is computed locally in dendritic branches at a stage before ganglion cells.

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Directionally selective calcium signals in dendrites of starburst amacrine cells

Retinal bipolar cells are the first 'projection neurons' of the vertebrate visual system — all of the information needed for vision is relayed by this intraretinal connection. Each of the at least 13 distinct types of bipolar cells systematically transforms the photoreceptor input in a different way, thereby generating specific channels that encode stimulus properties, such as polarity, contrast, temporal profile and chromatic composition. As a result, bipolar cell output signals represent elementary 'building blocks' from which the microcircuits of the inner retina derive a feature-oriented description of the visual world.

https://tombaden.files.wordpress.com/2013/07/2014-euler-et-al-nat-rev-neurosci.pdf

Retinal bipolar cells: elementary building blocks of vision.

We studied the morphology of bipolar cells in fixed vertical tissue sections of the rat retina by injecting the cells with Lucifer Yellow and neurobiotin. In addition to the rod bipolar cell, nine different putative cone bipolar cell types were distinguished according to the position of their somata in the inner nuclear layer and the branching pattern and stratification level of their axon terminals in the inner plexiform layer. Some of these bipolar cell populations were labeled immunocytochemically in vertical and horizontal sections using antibodies against the calcium-binding protein recoverin, the glutamate transporter GLT-1, the alpha isoform of the protein kinase C, and the Purkinje cell marker L7. These immunocytochemically labeled cell types were characterized in terms of cell density and distribution. We found that rod bipolar cells and GLT-1-positive cone bipolar cells occur at higher densities in a small region located in the upper central retina. This area probably corresponds to the central area, which is the region of highest ganglion cell density. A second peak of rod bipolar cell density in the lower temporal periphery matches the retinal area of binocular overlap. The population densities of the immunocytochemically characterized bipolar cells indicate that at least 50% of all bipolar cells are cone bipolar cells. The variety and total number of cone bipolar cells is surprising because the retina of the rat contains 99% rods. Our findings suggest that cone bipolar cells may play a more important role in the visual system of the rat than previously thought. o 1995 Wiley-Liss, Inc. Indexing terms: mammalian retina, recoverin immunoreactivity, glutamate transporter (GLT-1) immunoreactivity, PKC immunoreactivity, L7 immunoreactivity

Immunocytochemical identification of cone bipolar cells in the rat retina

The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before.

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Thomas Euler

Papers

The functional diversity of retinal ganglion cells in the mouse

Directionally selective calcium signals in dendrites of starburst amacrine cells

Retinal bipolar cells: elementary building blocks of vision.

Immunocytochemical identification of cone bipolar cells in the rat retina

Open labware: 3-D printing your own lab equipment