Christopher Eddy
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View article: COEXIST: Coordinated single-cell integration of serial multiplexed tissue images
COEXIST: Coordinated single-cell integration of serial multiplexed tissue images Open
Multiplexed tissue imaging (MTI) and other spatial profiling technologies commonly utilize serial tissue sectioning to comprehensively profile samples by imaging each section with unique biomarker panels or assays. The dependence on serial…
View article: COEXIST: Coordinated single-cell integration of serial multiplexed tissue images
COEXIST: Coordinated single-cell integration of serial multiplexed tissue images Open
Multiplexed tissue imaging (MTI) and other spatial profiling technologies commonly utilize serial tissue sectioning to comprehensively profile samples by imaging each section with unique biomarker panels or assays. The dependence on serial…
View article: Facilitating cell segmentation with the projection-enhancement network
Facilitating cell segmentation with the projection-enhancement network Open
Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly r…
View article: ADAD1 is required for normal translation of nuclear pore and transport protein transcripts in spermatids of<i>Mus musculus</i>
ADAD1 is required for normal translation of nuclear pore and transport protein transcripts in spermatids of<i>Mus musculus</i> Open
ADAD1 is a testis-specific RNA-binding protein expressed in post-meiotic spermatids whose loss leads to defective sperm and male infertility. However, the drivers of the Adad1 phenotype remain unclear. Morphological and functional analysis…
View article: The Projection-Enhancement Network (PEN)
The Projection-Enhancement Network (PEN) Open
Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly r…
View article: MDA-MB-231 Spheroid Z-stack
MDA-MB-231 Spheroid Z-stack Open
Single time image of MDA-MB-231 GFP spheroid after 22 hours of invasion into 1.5 mg/mL collagen. Imaged Leica TCS-SPE confocal microscope with 0.538 micron/pixel resolution in x-y dimension, 10 um in the z-direction.
View article: The mechanics and dynamics of cancer cells sensing noisy 3D contact guidance
The mechanics and dynamics of cancer cells sensing noisy 3D contact guidance Open
Significance The spatial organization of ECM fibers biases the polarization and migration of cancer cells, a phenomenon known as contact guidance which is directly linked to the clinical outcome of cancers. In physiological conditions, ECM…
View article: Modeling multicellular dynamics regulated by extracellular-matrix-mediated mechanical communication via active particles with polarized effective attraction
Modeling multicellular dynamics regulated by extracellular-matrix-mediated mechanical communication via active particles with polarized effective attraction Open
Collective cell migration is crucial to many physiological and pathological processes such as embryo development, wound healing, and cancer invasion. Recent experimental studies have indicated that the active traction forces generated by m…
View article: Extracellular Matrix regulates the morphodynamics of 3D migrating cancer cells
Extracellular Matrix regulates the morphodynamics of 3D migrating cancer cells Open
Cell shape is linked to cell function. The significance of cell morphodynamics, namely the temporal fluctuation of cell shape, is much less understood. Here we study the morphodynamics of MDA-MB-231 cells in type I collagen extracellular m…
View article: MDA-MB-231 Morphology Training and Test Sets
MDA-MB-231 Morphology Training and Test Sets Open
Text file format contains measurements from binary images of training and test set examples of five cancer cell migration modes observed in MDA-MB-231 cells in 3D migration. Class 0 = actin-enriched leading edge. Class 1 = Filopodia. Class…
View article: MDA-MB-231 Morphology Training and Test Sets
MDA-MB-231 Morphology Training and Test Sets Open
Text file format contains measurements from binary images of training and test set examples of five cancer cell migration modes observed in MDA-MB-231 cells in 3D migration. Class 0 = actin-enriched leading edge. Class 1 = Filopodia. Class…
View article: Training and Test Sets
Training and Test Sets Open
Text file format contains measurements from binary images of training and test set examples of five cancer cell migration modes observed in MDA-MB-231 cells in 3D migration. Class 0 = actin-enriched leading edge. Class 1 = Filopodia. Class…
View article: An Investigation of Higher Capacity Urban Freight Vehicles
An Investigation of Higher Capacity Urban Freight Vehicles Open
Studies have shown that increasing the capacity of Heavy Goods Vehicles is one of the most effective ways of reducing fuel consumption per tonne-kilometre of freight moved, with consequent reductions in greenhouse and noxious emissions. So…
View article: Collective dynamics and self-organization of active particles on random networks
Collective dynamics and self-organization of active particles on random networks Open
Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM fib…
View article: The morphodynamics of 3D migrating cancer cells
The morphodynamics of 3D migrating cancer cells Open
Cell shape is an important biomarker that is directly linked to cell function. However, cell morphodynamics, namely the temporal fluctuation of cell shape is much less understood. We study the morphodynamics of MDA-MB-231 cells in type I c…
View article: Research data supporting 'Camera-based measurement of cyclist motion'
Research data supporting 'Camera-based measurement of cyclist motion' Open
A set of .fig files, that can be opened by Matlab or Octave, providing all data needed to generate the figures in the paper.
View article: Filopodia SVM validation set
Filopodia SVM validation set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Filopodia SVM test set
Filopodia SVM test set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Small-bleb SVM test set
Small-bleb SVM test set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Actin-enriched leading edge SVM test set
Actin-enriched leading edge SVM test set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Hemi-sphere bleb SVM test set
Hemi-sphere bleb SVM test set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Lamellipodia SVM validation set
Lamellipodia SVM validation set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Actin-enriched leading edge SVM training images
Actin-enriched leading edge SVM training images Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Filopodia SVM training images
Filopodia SVM training images Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Hemi-sphere bleb SVM validation set
Hemi-sphere bleb SVM validation set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).
View article: Hemi-sphere bleb deep learning training set
Hemi-sphere bleb deep learning training set Open
Grayscale images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Images have been background subtracted (ImageJ: 50 pixel radius rolling ball). Cells manually classified based on morphology alone (no staining).
View article: Actin-enriched leading edge deep learning training set
Actin-enriched leading edge deep learning training set Open
Grayscale images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Images have been background subtracted (ImageJ: 50 pixel radius rolling ball). Cells manually classified based on morphology alone (no staining).
View article: Actin-enriched leading edge SVM validation set
Actin-enriched leading edge SVM validation set Open
Binary images of MDA-MB-231 GFP cells in 3D Collagen-I matrices. Cells manually classified based on morphology alone (no staining).