Understanding the Influence of Receptive Field and Network Complexity in Neural-Network-Guided TEM Image Analysis

Trained neural networks are promising tools to analyze the ever-increasing amount of scientific image data, but it is unclear how to best customize these networks for the unique features in transmission electron micrographs. Here, we systematically examine how neural network architecture choices affect how neural networks segment, or pixel-wise separate, crystalline nanoparticles from amorphous background in transmission electron microscopy (TEM) images. We focus on decoupling the influence of receptive field, or the area of the input image that contributes to the output decision, from network complexity, which dictates the number of trainable parameters. We find that for low-resolution TEM images which rely on amplitude contrast to distinguish nanoparticles from background, the receptive field does not significantly influence segmentation performance. On the other hand, for high-resolution TEM images which rely on a combination of amplitude and phase contrast changes to identify nanoparticles, receptive field is a key parameter for increased performance, especially in images with minimal amplitude contrast. Our results provide insight and guidance as to how to adapt neural networks for applications with TEM datasets.Comment: 11 pages, 8 figure

Mechanisms underlying homeostatic plasticity in the Drosophila mushroom body in vivo

Neural network function requires an appropriate balance of excitation and inhibition to be maintained by homeostatic plasticity. However, little is known about homeostatic mechanisms in the intact central brain in vivo. Here, we study homeostatic plasticity in the Drosophila mushroom body, where Kenyon cells receive feedforward excitation from olfactory projection neurons and feedback inhibition from the anterior paired lateral neuron (APL). We show that prolonged (4-d) artificial activation of the inhibitory APL causes increased Kenyon cell odor responses after the artificial inhibition is removed, suggesting that the mushroom body compensates for excess inhibition. In contrast, there is little compensation for lack of inhibition (blockade of APL). The compensation occurs through a combination of increased excitation of Kenyon cells and decreased activation of APL, with differing relative contributions for different Kenyon cell subtypes. Our findings establish the fly mushroom body as a model for homeostatic plasticity in vivo

Engineering the Photoresponse of InAs Nanowires

We report on individual-InAs nanowire optoelectronic devices which can be tailored to exhibit either negative or positive photoconductivity (NPC or PPC). The NPC photoresponse time and magnitude is found to be highly tunable by varying the nanowire diameter under controlled growth conditions. Using hysteresis characterization, we decouple the observed photoexcitation-induced hot electron trapping from conventional electric field-induced trapping to gain a fundamental insight into the interface trap states responsible for NPC. Furthermore, we demonstrate surface passivation without chemical etching which both enhances the field-effect mobility of the nanowires by approximately an order of magnitude and effectively eliminates the hot carrier trapping found to be responsible for NPC, thus restoring an "intrinsic" positive photoresponse. This opens pathways toward engineering semiconductor nanowires for novel optical-memory and photodetector applications.We acknowledge funding from the EPSRC (Grant No. EP/ M009505/1) and the ERC (Grant No. 716471, ACrossWire). S.H. acknowledges funding from the EPSRC (Grant No. EP/ P005152/1). This work was also supported by the Australian Research Council, Australian National Fabrication Facility and Australian Microscopy & Microanalysis Research Facility. J.A.A.-W. acknowledges the support of his Research Fellowships from the Royal Commission for the Exhibition of 1851 and Churchill College, Cambridge. C.K.G acknowledges the support of her scholarship from The Winston Churchill Foundation of the United States

ATP release via anion channels

ATP serves not only as an energy source for all cell types but as an ‘extracellular messenger-for autocrine and paracrine signalling. It is released from the cell via several different purinergic signal efflux pathways. ATP and its Mg2+ and/or H+ salts exist in anionic forms at physiological pH and may exit cells via some anion channel if the pore physically permits this. In this review we survey experimental data providing evidence for and against the release of ATP through anion channels. CFTR has long been considered a probable pathway for ATP release in airway epithelium and other types of cells expressing this protein, although non-CFTR ATP currents have also been observed. Volume-sensitive outwardly rectifying (VSOR) chloride channels are found in virtually all cell types and can physically accommodate or even permeate ATP4- in certain experimental conditions. However, pharmacological studies are controversial and argue against the actual involvement of the VSOR channel in significant release of ATP. A large-conductance anion channel whose open probability exhibits a bell-shaped voltage dependence is also ubiquitously expressed and represents a putative pathway for ATP release. This channel, called a maxi-anion channel, has a wide nanoscopic pore suitable for nucleotide transport and possesses an ATP-binding site in the middle of the pore lumen to facilitate the passage of the nucleotide. The maxi-anion channel conducts ATP and displays a pharmacological profile similar to that of ATP release in response to osmotic, ischemic, hypoxic and salt stresses. The relation of some other channels and transporters to the regulated release of ATP is also discussed

Understanding the Influence of Receptive Field and Network Complexity in Neural Network-Guided TEM Image Analysis.

Trained neural networks are promising tools to analyze the ever-increasing amount of scientific image data, but it is unclear how to best customize these networks for the unique features in transmission electron micrographs. Here, we systematically examine how neural network architecture choices affect how neural networks segment, or pixel-wise separate, crystalline nanoparticles from amorphous background in transmission electron microscopy (TEM) images. We focus on decoupling the influence of receptive field, or the area of the input image that contributes to the output decision, from network complexity, which dictates the number of trainable parameters. For low-resolution TEM images which rely on amplitude contrast to distinguish nanoparticles from background, we find that the receptive field does not significantly influence segmentation performance. On the other hand, for high-resolution TEM images which rely on both amplitude and phase-contrast changes to identify nanoparticles, receptive field is an important parameter for increased performance, especially in images with minimal amplitude contrast. Rather than depending on atom or nanoparticle size, the ideal receptive field seems to be inversely correlated to the degree of nanoparticle contrast in the image. Our results provide insight and guidance as to how to adapt neural networks for applications with TEM datasets

Trypsin increases availability and open probability of cardiac L-type Ca2+ channels without affecting inactivation induced by Ca2+.

The patch-clamp technique was employed to investigate the response of single L-type Ca2+ channels to the protease trypsin applied to the intracellular face of excised membrane patches from guinea pig ventricular myocytes. Calpastatin and ATP were used to prevent run-down of Ca2+ channel activity monitored with 96 mM Ba2+ as charge carrier in the presence of 2.5 microM (-)-BAYK 8644. Upon application of trypsin (100 micrograms/ml) channel activity was enhanced fourfold and remained elevated upon removal of trypsin, as expected of a proteolytic, irreversible modification. The trypsin effect was not mediated by a proteolytic activation of protein kinases, as evidenced by the insensitivity of this effect to protein kinase inhibitors. Trypsin-modified Ca2+ channels exhibited the usual run-down phanomenon upon removal of calpastatin and ATP. In ensemble average currents trypsin-induced changes of channel function are apparent as a threefold increase in peak current and a reduction in current inactivation. At the single channel level these effects were based on about a twofold increase in both Ca2+ channels' availability and open probability. Neither the actual number of channels in the patch nor their unitary conductance as well as reversal potential was changed by trypsin. The Ca(2+)-induced inactivation was not impaired, as judged by a comparable sensitivity of trypsin-modified Ca2+ channels to intracellular Ca2+. Similarly, trypsin treatment did not affect the sensitivity of Ca2+ channels to phenylalkylmine inhibition. The observed alterations in channel function are discussed in terms of possible structural correlates