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Resources. AutoQuant Citations Confocal Deconvolution: Regulation of Focal Adhesion Kinase Activation, Breast Cancer Cell Motility, and Amoeboid Invasion.

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Presentation on theme: "Resources. AutoQuant Citations Confocal Deconvolution: Regulation of Focal Adhesion Kinase Activation, Breast Cancer Cell Motility, and Amoeboid Invasion."— Presentation transcript:

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2 AutoQuant Citations Confocal Deconvolution: Regulation of Focal Adhesion Kinase Activation, Breast Cancer Cell Motility, and Amoeboid Invasion by the RhoA Guanine Nucleotide Exchange Factor Net1 Regulation of Focal Adhesion Kinase Activation, Breast Cancer Cell Motility, and Amoeboid Invasion by the RhoA Guanine Nucleotide Exchange Factor Net1 HS Carr, Y Zuo, W Oh, JA Frost – Mole. and cell. biology, 2013 - Am Soc Microbiol Electrophysiological changes precede morphological changes to frontal cortical pyramidal neurons in the rTg4510 mouse model of progressive tauopathy Electrophysiological changes precede morphological changes to frontal cortical pyramidal neurons in the rTg4510 mouse model of progressive tauopathy JL Crimins, AB Rocher, JI Luebke - Acta neuropathologica, 2012 – Springer Tumor Necrosis Factor Alpha Mediates GABA A Receptor Trafficking to the Plasma Membrane of Spinal Cord Neurons In Vivo Tumor Necrosis Factor Alpha Mediates GABA A Receptor Trafficking to the Plasma Membrane of Spinal Cord Neurons In Vivo ED Stück, RN Christensen, JR Huie, CA Tovar… - Neural …, 2012 - hindawi.comJR Huie 3D dendritic spine automatic detection and segmentation through samples obtained by confocal microscopy 3D dendritic spine automatic detection and segmentation through samples obtained by confocal microscopy L Fernández-Soria… - … Computing and Simulation …, 2012 - ieeexplore.ieee.org The spatial organization and extraction of the wall-forming bodies of Eimeria maxima S Froelich, M Johnson, M Robinson… - …, 2013 - Cambridge Univ Press Google Scholar shows 299 results since 2012 for “AutoQuant Software”

3 AutoQuant Citations Confocal Deconvolution highlight: Tumor Necrosis Factor Alpha Mediates GABA A Receptor Trafficking to the Plasma Membrane of Spinal Cord Neurons In Vivo Tumor Necrosis Factor Alpha Mediates GABA A Receptor Trafficking to the Plasma Membrane of Spinal Cord Neurons In Vivo ED Stück, RN Christensen, JR Huie, CA Tovar… - Neural …, 2012 - hindawi.comJR Huie “Performing deconvolution on confocal image stacks allowed for greater resolution…than was possible with either [wide-field or confocal] technique alone.” Google Scholar shows 299 results since 2012 for “AutoQuant Software” RawDeconvolved After only 3 iterations

4 AutoQuant Citations Super Resolution Deconvolution: Super-Resolution Microscopy of the Neuronal Calcium-Binding Proteins Calneuron-1 and Caldendrin Super-Resolution Microscopy of the Neuronal Calcium-Binding Proteins Calneuron-1 and Caldendrin J Hradsky, M Mikhaylova, A Karpova… - Binding Proteins and …, 2013 – Springer Inner membrane dynamics in mitochondria D Dikov, J Bereiter-Hahn - Journal of Structural Biology, 2013 – Elsevier Capturing the surface texture and shape of pollen: A comparison of microscopy techniques M Sivaguru, L Mander, G Fried, SW Punyasena - PloS one, 2012 - dx.plos.org Google Scholar shows 299 results since 2012 for “AutoQuant Software”

5 AutoQuant Citations Non-standard deconvolution highlight: Non-scanning motionless fluorescence three-dimensional holographic microscopy J Rosen, G Brooker – Nature Photonics – 2008 – Nature Features the use of AutoQuant to deconvolve an unsupported modality: holographic microscopy. A measured PSF and non-blind deconvolution were used. “The deconvolved FINCHSCOPE images show quite similar information to that obtained when the same specimen was imaged on a…spinning disk confocal system; however, the FINCHSCOPE could obtain the data about 25 times faster.” Google Scholar shows 299 results since 2012 for “AutoQuant Software” RawDeconvolved

6 Comparison Publications Comparison of deconvolution software in 3d microscopy. a user point of view part 1 A Griffa, N Garin, D Sage - GIT Imaging & Microscopy, 2010 - infoscience.epfl.ch 3D deconvolution of spherically aberrated images using commercial software MA Model, J Fang, P Yuvaraj, Y Chen… - Journal of …, 2011 - Wiley Online Library Deconvolution microscopy JB Sibarita - Microscopy Techniques, 2005 - Springer

7 Calibration of Wide-Field Deconvolution Microscopy for Quantitative Fluorescence Imaging J Lee, T Wee, C Brown – Journal of Biomolecular Techniques – 2014 - ABRF Follows “best practices” for image collection. Measures multiple sets of bead collections in Imaris before and after deconvolution. Intensity analysis determines that “… the deconvolved images clearly indicate that deconvolution using the AutoQuant X3 blind deconvolution algorithm preserves the relative quantitative intensity data.” Volume analysis finds that “deconvolution decreased the measured volume to 70% of the original image volumes, which is much closer to the expected volume… based on the actual microsphere size.” Validation Publication RawDeconvolved “We are now confident that the use of AutoQuant X3 is appropriate and accurate for quantitative fluorescence imaging.”

8 AutoQuant Publications Holmes, T. J. (1991). Acceleration of Maximum-Likelihood Image-Restoration for Fluorescence Microscopy and Other Noncoherent Imagery. J of the Opt Soc. 8(6). 893- 907 Iteration Acceleration Description Holmes, T. J. (1991). Acceleration of Maximum-Likelihood Image-Restoration for Fluorescence Microscopy and Other Noncoherent Imagery. J of the Opt Soc. 8(6). 893- 907 Holmes, T. J., “Light Microscopic Images Reconstructed by MLE, Ch 24 Handbook of Bio CF Microscopy, James Pawley, 1995 Holmes, T. J., “Light Microscopic Images Reconstructed by MLE, Ch 24 Handbook of Bio CF Microscopy, James Pawley, 1995 Maximum Likelihood Estimation (MLE) Description Holmes, T. J. (1992). "Blind Deconvolution of Quantum-Limited Incoherent Imagery." Journal of the Optical Society of America A. 9(7): 1052-1061. Blind Deconvolution Description Holmes, T. J. (1992). "Blind Deconvolution of Quantum-Limited Incoherent Imagery." Journal of the Optical Society of America A. 9(7): 1052-1061. Gibson, S. F. and F. Lanni. (1991). "Experimental Test of an Analytical Model of Aberration in an Oil-Immersion Objective Lens Used in Three-Dimensional Light Microscopy." Journal of the Optical Society of America A. 8(10): 1601-1613. Gibson, S. F. and F. Lanni. (1991). "Experimental Test of an Analytical Model of Aberration in an Oil-Immersion Objective Lens Used in Three-Dimensional Light Microscopy." Journal of the Optical Society of America A. 8(10): 1601-1613. Spherical Aberration Description

9 New White Paper Six-label Imaging of Brain Tissue: Spectral & Multiphoton Imaging with Deconvolution New White Paper from Wadsworth Center http://www.mediacy.com/index.aspx?page=Auto_App_3DSpectral

10 New Training Handbook

11 Basics of Deconvolution 3D Deconvolution Methods PSF Settings 3D Settings Output Settings Expert Settings Adaptive vs Fixed Noise Handling Sperical Aberration Validation of Results FTP Download

12 Demo Images to use Provided by FTP

13 Demo Images to use Multi-Photon Confocall Beads Widefieldl Confocall Widefield

14 Resource Availability - FTP Brochure: ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Brochure/AutoQuant X3 Brochure - 6pages.pdf Demo Images: ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Demo Images/LeftSetBottom.zip ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Demo Images/MultiPhoton.zip ftp://ftp.mediacy.com/uploaded/AQX300 Sales Demo Images/Widefield/Rat-Brain.zip ftp://ftp.mediacy.com/uploaded/AQX300 Sales Demo Images/CARV.zip Documentation: ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Documentation/AutoQuant X Training Handbook v1.3_rev2.pdf ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Documentation/AutoQuant X3 User Guide.pdf ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 Documentation/Quick Start X3.pdf Powerpoints: ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 PPTs/AQX3_Resources.pptx ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 PPTs/AQX3_Resources.pptx ftp://ftp.mediacy.com/uploaded/AQX_BitPlane/AQX3 PPTs/AQX3 - New Features Overview.pptx

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