Deep orthogonal multi-wavelength fusion for tomogram-free diagnosis in diffuse optical imaging.

Novel portable diffuse optical tomography (DOT) devices for breast cancer lesions hold great promise for non-invasive, non-ionizing breast cancer screening. Critical to this capability is not just the identification of lesions but rather the complex problem of discriminating between malignant and benign lesions. To accurately reconstruct the highly heterogeneous tissue of a cancer lesion in healthy breast tissue using DOT, multiple wavelengths can be leveraged to maximize signal penetration while minimizing sensitivity to noise.

Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts.

Identification and morphological analysis of mitochondria-ER contacts (MERCs) by fluorescent microscopy is limited by subpixel resolution interorganelle distances. Here, the membrane contact site (MCS) detection algorithm, MCS-DETECT, reconstructs subpixel resolution MERCs from 3D super-resolution image volumes. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria-ER linker expression in COS-7 cells.

DataCurator.jl: efficient, portable and reproducible validation, curation and transformation of large heterogeneous datasets using human-readable recipes compiled into machine-verifiable templates.

Large-scale processing of heterogeneous datasets in interdisciplinary research often requires time-consuming manual data curation. Ambiguity in the data layout and preprocessing conventions can easily compromise reproducibility and scientific discovery, and even when detected, it requires time and effort to be corrected by domain experts. Poor data curation can also interrupt processing jobs on large computing clusters, causing frustration and delays.

SPECHT: Self-tuning Plausibility based object detection Enables quantification of Conflict in Heterogeneous multi-scale microscopy.

Identification of small objects in fluorescence microscopy is a non-trivial task burdened by parameter-sensitive algorithms, for which there is a clear need for an approach that adapts dynamically to changing imaging conditions. Here, we introduce an adaptive object detection method that, given a microscopy image and an image level label, uses kurtosis-based matching of the distribution of the image differential to express operator intent in terms of recall or precision. We show how a theoretical upper bound of the statistical distance in feature space enables application of belief theory to obtain statistical support for each detected object, capturing those aspects of the image that support the label, and to what extent.

Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS.

Mitochondria are major sources of cytotoxic reactive oxygen species (ROS), such as superoxide and hydrogen peroxide, that when uncontrolled contribute to cancer progression. Maintaining a finely tuned, healthy mitochondrial population is essential for cellular homeostasis and survival. Mitophagy, the selective elimination of mitochondria by autophagy, monitors and maintains mitochondrial health and integrity, eliminating damaged ROS-producing mitochondria.

Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography.

Diffuse optical tomography (DOT) leverages near-infrared light propagation through tissue to assess its optical properties and identify abnormalities. DOT image reconstruction is an ill-posed problem due to the highly scattered photons in the medium and the smaller number of measurements compared to the number of unknowns. Limited-angle DOT reduces probe complexity at the cost of increased reconstruction complexity.

Super resolution microscopy and deep learning identify Zika virus reorganization of the endoplasmic reticulum.

The endoplasmic reticulum (ER) is a complex subcellular organelle composed of diverse structures such as tubules, sheets and tubular matrices. Flaviviruses such as Zika virus (ZIKV) induce reorganization of ER membranes to facilitate viral replication. Here, using 3D super resolution microscopy, ZIKV infection is shown to induce the formation of dense tubular matrices associated with viral replication in the central ER.

ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy.

Single molecule localization microscopy (SMLM) allows unprecedented insight into the three-dimensional organization of proteins at the nanometer scale. The combination of minimal invasive cell imaging with high resolution positions SMLM at the forefront of scientific discovery in cancer, infectious, and degenerative diseases. By stochastic temporal and spatial separation of light emissions from fluorescent labelled proteins, SMLM is capable of nanometer scale reconstruction of cellular structures.