Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.

Preclinical studies of psychiatric disorders require the use of animal models to investigate the impact of environmental factors or genetic mutations on complex traits such as decision-making and social interactions. Here, we present a real-time method for behavior analysis of mice housed in groups that couples computer vision, machine learning and Triggered-RFID identification to track and monitor animals over several days in enriched environments. The system extracts a thorough list of individual and collective behavioral traits and provides a unique phenotypic profile for each animal. On mouse models, we study the impact of mutations of genes Shank2 and Shank3 involved in autism. Characterization and integration of data from behavioral profiles of mutated female mice reveals distinctive activity levels and involvement in complex social configuration.

Elucidating protein functions and molecular organisation requires to localise precisely single or aggregated molecules and analyse their spatial distributions. We develop a statistical method SODA (Statistical Object Distance Analysis) that uses either micro- or nanoscopy to significantly improve on standard co-localisation techniques. Our method considers cellular geometry and densities of molecules to provide statistical maps of isolated and associated (coupled) molecules. We use SODA with three-colour structured-illumination microscopy (SIM) images of hippocampal neurons, and statistically characterise spatial organisation of thousands of synapses. We show that presynaptic synapsin is arranged in asymmetric triangle with the 2 postsynaptic markers homer and PSD95, indicating a deeper localisation of homer. We then determine stoichiometry and distance between localisations of two synaptic vesicle proteins with 3D-STORM. These findings give insights into the protein organisation at the synapse, and prove the efficiency of SODA to quantitatively assess the geometry of molecular assemblies.

We present a novel bioimage informatics workflow that combines Icy and Cytomine software and their algorithms to enable large-scale analysis of digital slides from multiple sites. In particular, we apply this workflow on renal biopsies and evaluate empirically our approach for the automatic detection of glomeruli in hundreds of tissue sections.

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Preclinical studies of psychiatric disorders require the use of animal models to investigate the impact of environmental factors or genetic mutations on complex traits such as decision-making and social interactions. Here, we present a real-time method for behavior analysis of mice housed in groups that couples computer vision, machine learning and Triggered-RFID identification to track and monitor animals over several days in enriched environments. The system extracts a thorough list of individual and collective behavioral traits and provides a unique phenotypic profile for each animal. On mouse models, we study the impact of mutations of genes Shank2 and Shank3 involved in autism. Characterization and integration of data from behavioral profiles of mutated female mice reveals distinctive activity levels and involvement in complex social configuration. RESULTSWe have designed an integrated system that tracks and monitors, for either hours or days, the activities of four mice in a rich environment (Supplementary movie -Method overview). This system determines the outline mask and orientation of each mouse and builds, from these data, a comprehensive repertoire of individual and social behavioral events. The system can track mice of any coat color in a rich environment. It is robust to the presence of food, water, sawdust, brown crinkle paper, white compressed cotton cylinders, toys and house (either transparent to infrared or opaque) (Fig. 1a). The tracking ( Supplementary Fig. S1 -Tracking diagram) is performed by using an RGBD camera, filming the mice from the top (Fig. 1b). The 2D ½ data (infra-red intensity and distance from the sensor of each pixel acquired; Fig. 1c-d, Supplementary methods -Capturing depth map) are integrated to compute a background depth map ( Fig. 1e), which is a representation of the environment where the mice have been computationally removed (Supplementary methods -Computing the background height-map; Supplementary movie -Background height-map demo). The segmentation ( Fig. 1f-g) step that extracts objects and boundaries is performed on an image obtained by subtracting the current acquisition from the background height-map (Supplementary methods -Segmentation and detection). Segmentations are then filtered by a dedicated machine learning to reject detections that do not match the mice (Supplementary methods -Building the detection feature vector, Detection filtering with machine learning) and detections are then processed to separate mice that are in contact (Supplementary methods -Detection splitter). Extraction of additional data such as the orientation (Supplementary methods -Head/tail detection post-processing) or the detection of ears, eyes and nose are then performed ( Fig. 1f-g, Supplementary methods -Head sub-parts detection) thus enabling the detection of the tilt-orientation of the head. Detections are then processed for tracking (Supplementary methods -Tracking extender association process). Identity of tracks is retrieved in real-time by combining machine learning (Suppleme...

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Metabolic studies and animal knockout models point to the critical role of polyunsaturated docosahexaenoic acid (22:6, DHA)-containing phospholipids (PLs) in physiology. Here, we investigated the impact of DHA-PLs on the dynamics of transendothelial cell macroapertures (TEMs) triggered by RhoA inhibition-associated cell spreading. Lipidomic analyses show that human umbilical vein endothelial cells (HUVECs) subjected to DHA-diet undergo a 6-fold enrichment in DHA-PLs at plasma membrane (PM) at the expense of monounsaturated OA-PLs. Consequently, DHA-PLs enrichment at the PM induces a reduction of cell thickness and shifts cellular membranes towards a permissive mode of membrane fusion for transcellular tunnel initiation. We provide evidence that a global homeostatic control of membrane tension and cell cortex rigidity minimizes overall changes of TEM area through a decrease of TEM size and lifetime. Conversely, low DHA-PL levels at the PM leads to the opening of unstable and wider TEMs. Together, this provides evidence that variations of DHA-PLs levels in membranes affect cell biomechanical properties.