Explore projects
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Code and data for paper: Dempsey W. P., Hodas N. O., Ponti A. and Pantazis P. Determination of the source of SHG verniers in zebrafish skeletal muscle. Scientific Reports 5:18119. 2015.
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This is the GUI for CellX, a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images.
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Supplementary code for the paper: Aizhan Tastanova et al. "A biomedical tattoo system for early detection of cancer-associated hypercalcemia".
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Collection of third-party tools and libraries for MATLAB.
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Zhang et al. Notch2 signaling regulates Id4 and cell cycle genes to maintain neural stem cell quiescence in the adult hippocampus.
Collaboration with Taylor Lab
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IceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris (http://www.bitplane.com) and MATLAB (http://www.mathworks.com) using the Imaris XT interface (http://www.bitplane.com/go/products/imarisxt).
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MATLAB wrapper around the Java Bio-Formats library (https://www.openmicroscopy.org/bio-formats/).
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Application of global two stage methodology to single cell data to infer kinetic Non-linear mixed effect models of signalling.
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Application of global two stage methodology to single cell data to infer kinetic Non-linear mixed effect models of signalling.
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Software for embryo alignment, segmentation and lineage tracing using dual fluorescent labels with primed conversion.
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Code for the paper: Welling, Mohr, et al. "Primed Track, high-fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins".
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A Specialized ODE Integrator for the Efficient Computation of Parameter Sensitivities
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Vetter, Kokic et al. Aboav-Weaire’s law in epithelia results from an angle constraint in contiguous polygonal lattices
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Kokic et al. Minimisation of surface energy drives apical epithelial organisation and gives rise to Lewis’ law
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