Autoquant x3

Manufactured by Media Cybernetics

Sourced in United States, Switzerland

AutoQuant X3 is a software application that provides advanced image analysis and processing capabilities. It offers a range of tools for visualizing, quantifying, and interpreting digital microscopy images.

Automatically generated - may contain errors

Lab products found in correlation

Orca flash 4.0 v3, by Olympus (3 mentions) Matlab, by MathWorks (2 mentions) Sp5 confocal microscope, by Leica (2 mentions) Sp5 laser scanning confocal microscope, by Leica (2 mentions) Eclipse ti, by Nikon (2 mentions) Lsm 780, by Zeiss (2 mentions) Metamorph software, by Molecular Devices (2 mentions) Dmi6000b microscope, by Leica (2 mentions) Tcs sp2 aobs confocal laser scanning imaging system, by Leica (2 mentions) Imagem c9100 13, by Hamamatsu Photonics (2 mentions) Delta vision elite microscope system, by GE Healthcare (2 mentions) Plapon, by Olympus (2 mentions) Ix3 zdc2, by Olympus (2 mentions) Stage top incubator, by Tokai Hit (2 mentions) Uapon 150xotirf, by Olympus (2 mentions) H 1500, by Vector Laboratories (2 mentions) Anti cb1, by Abcam (2 mentions) Fluoview fv1000 confocal laser scanning microscope, by Olympus (2 mentions) Anti ago2 antibody, by Fujifilm (2 mentions) Ix83 fluorescence microscope system, by Olympus (2 mentions)

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AutoQuant (37 citations) AutoQuant X3 Deconvolution Software (3 citations)

78 protocols using autoquant x3

Astrocyte Morphometric Analysis with Imaging

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High NA diffraction-limited confocal microscopy images of isolated astrocytes were analyzed using Fiji, Vaa3D^{57 (link)}, Matlab (MathWorks, USA), and Autoquant X3.1 (Media Cybernetics, USA). Astrocyte arbors were reconstructed using the Vaa3D-Neuron2 Auto Tracing Based on APP2 plugin and their structure was sorted using the sort neuron SWC plugin. SWC were exported to Matlab using the TREES toolbox and the model was resized to the real dimensions from the initial acquisition. Finally, information from the model was extracted using L-measure^{58 (link)}.

Clavreul S., Abdeladim L., Hernández-Garzón E., Niculescu D., Durand J., Ieng S.H., Barry R., Bonvento G., Beaurepaire E., Livet J, & Loulier K. (2019). Cortical astrocytes develop in a plastic manner at both clonal and cellular levels. Nature Communications, 10, 4884.

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ABCA3-eGFP Confocal Microscopy in A549 Cells

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Confocal microscopy of A549 cells transfected with ABCA3-eGFP was done using an SP8 TCS laser scanning confocal microscope (Leica) equipped with a 63× 1.4 NA oil immersion objective and an environmental control chamber heated to 37 °C. Image analysis was performed in ImageJ/FIJI^{47 (link)}. Automated 3D segmentation of ABCA3-eGFP structures was done in Imaris 9.5.1 (Bitplane) after deconvolution in AutoQuant X3.1 (Media Cybernetics).

Klein S., Wimmer B.H., Winter S.L., Kolovou A., Laketa V, & Chlanda P. (2021). Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies. Communications Biology, 4, 137.

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3D Imaging of Neural Structures

Cited 2 times

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Sections were examined with a wide field fluorescent microscope (Zeiss AxioIamger) and cells or terminals mapped with a computer-assisted mapping program (Neurolucida, v 10; MicroBrightField, Williston, VT; RRID:nif-0000-10294) as previously described (Bochorishvili et al., 2012 (link); Abbott et al., 2013b (link)). Images were digitally captured with a Zeiss Mrc camera (1388×1040 resolution) and the resulting TIFF files were imported into the Canvas drawing software (v. 10, ACDC, Miami, FL). Output levels were adjusted to include all information-containing pixels. Balance and contrast was adjusted to reflect true rendering as much as possible. No other photo-retouching was done. Figures were assembled and labeled within the Canvas software. Z-stacks were constructed using the computer interface-motor-driven stage by capturing images using different filter sets at 0.3 micron z intervals through tissue depths of 5–10 microns. The resulting images were subjected to 3D blind deconvolution through 10 iterations using the AutoQuant X3 software (Media Cybernetics, Rockville, MD; RRID:SciRes_000125). Deconvoluted stacks were then processed with Volocity 3D image Analysis software (version 4.4, Improvision; RRID:SciRes_000112) for 3D rendering and confirmation of close appositions as detailed in (Holloway et al., 2013 (link)).

Bochorishvili G., Nguyen T., Coates M.B., Viar K.E., Stornetta R.L, & Guyenet P.G. (2014). The orexinergic neurons receive synaptic input from C1 cells in rats. The Journal of comparative neurology, 522(17), 3834-3846.

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Image Analysis and Centriole Measurements

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Image analysis and assembly was performed in Photoshop (Adobe) and Fiji (National Institute of Health, Bethesda, MD). Fiji and NIS‐Elements was used to measure signal intensity and centriole length and width. NIS‐Elements was used for surface rendering. AutoQuant X3 software (MediaCybernetics) was used for deconvolution of widefield images. Images were acquired under identical imaging settings for all samples within each experiment. The levels of fluorescent signals were sometimes differentially adjusted between different image panels, to improve the visibility of the dimmer signals. In some image panels, maximum intensity projections of all acquired Z slices spanning a part of the cell containing centrioles were presented. In some instances, to better illustrate centriole width and length or a specific point discussed in text, only central Z section is presented. The presentation method is indicated in figure legends or above figure panels.

SAHABANDU N., KONG D., MAGIDSON V., NANJUNDAPPA R., SULLENBERGER C., MAHJOUB M.R, & LONCAREK J. (2019). Expansion microscopy for the analysis of centrioles and cilia. Journal of Microscopy, 276(3), 145-159.

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Neuronal Morphology Visualization and Analysis

Cited 1 time

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Dendrites and cell body of fluorescent dentate neurons were traced using a computer-controlled microscope-based system (Axio Imager A2 Zeiss microscope, 100X oil-immersion objective) with a software (Neurolucida® software; MicroBrigthField Bioscience) that provides neuron tracing tools to trace from a live camera image (QImaging).
For spine analysis, confocal stacks of images were obtained with a Leica SP5 confocal microscope (63X oil-immersion objective; XY dimensions: 41.0 μm; z-axis interval: 0.13 μm). The dendritic length of each segment was measured on Z projections, and the number of dendritic spines was counted using NeuronStudio software ^{35 (link)}. Before spine analysis, images were deconvoluted using AutoQuantX3 software (Media Cybernetics). A minimum of 30 dendritic segments per experimental group and time point were examined for spine analysis. Morphometric analysis of the AIS was done as previously described ^{36 (link)} using a Leica SP5 microscope (63X water-immersion objective; XY dimensions: 82.0 μm; z-axis interval: 0.21 μm).

Kerloch T., Farrugia F., Bouit L., Maître M., Terral G., Koehl M., Mortessagne P., Heng J.I., Blanchard M., Doat H., Leste-Lasserre T., Goron A., Gonzales D., Perrais D., Guillemot F., Abrous D.N, & Pacary E. (2021). The atypical Rho GTPase Rnd2 is critical for dentate granule neuron development and anxiety-like behavior during adult but not neonatal neurogenesis. Molecular Psychiatry, 26(12), 7280-7295.

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3D Reconstruction of Secretory Granules

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Prior to 3D reconstruction of SGs, all images were deconvoluted using AutoQuantX3 software (Media Cybernetics Inc.), and converted black and white by ImageJ33 34 (link). Then, 3D images of cells were constructed from serial confocal images using Neurolucida (64-bit; MBF Bioscience, Williston, VT, USA). Contours were abstracted automatically (beads, cell body and SGs) or semi-automatically (nucleus). For fine structures, contours were defined to be the area with 90–95% fluorescence intensity when the center and periphery of a negatively stained region were set to 0% and 100%, respectively. Each contour was linked to a contour at the same position in the neighboring image, and designated as a single structure. Abstracted and grouped contours were reconstructed in 3D by lamination at the intervals used to acquire the individual images. Size and volume were calculated from reconstructions using Neurolucida Explorer (MBF Bioscience).

Tanaka S, & Takakuwa Y. (2016). A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging. Scientific Reports, 6, 23369.

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Retinal Vascular Morphometry and Quantification

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To quantify the diameters of retinal arterioles and venules, collateral angles, arteriolar EC areas and Col IV, Laminin, αSMA, plasmatic albumin, VE-Cadherin, fibrillin-1, MAGP1, MAGP2 and elastin, a z-stack confocal series of 30 optical sections (x/y/z = 146.25 × 146.25 × 0.3 μm) were acquired with a 63× oil immersion objective. Acquisitions were performed at the area of the first collateral vessel bifurcation starting from the optic disc. The maximal intensity projections of the confocal stacks were analyzed using ImageJ software [28 (link)]. The diameters of retinal arterioles and venules were calculated from three different length measurements performed perpendicularly to the vessel axis at the first collateral vessel bifurcation. The collateral angles of retinal arterioles were determined (at the first collateral vessel bifurcation) using the ImageJ “Angle tool” function. The positive surface areas per field were measured on thresholded images and normalized to the IB4-positive surface area. For 3D reconstructions, confocal stacks were first deconvoluted using the AutoQuant X3 software (Media Cybernetics) and then processed for image reconstruction using IMARIS software (Bitplane).

Alonso F., Li L., Fremaux I., Reinhardt D.P, & Génot E. (2022). Fibrillin-1 Regulates Arteriole Integrity in the Retina. Biomolecules, 12(10), 1330.

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Quantitative Analysis of Cell Cultures

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For quantitative analysis of the percentage of area occupied by MEF-clover cells, images were analyzed by ImageJ 1.53c software (National Institute of Health, Bethesda, MD, USA) to obtain the percentage of area of interest. For quantitative analysis of the colocalized area of two types of fluorescent cells, images were analyzed by AutoQuant X3 software (Media Cybernetics Inc., Rockville, MD, USA) to obtain the percentage of colocalized area.

Peng Z., Hao M., Tong H., Yang H., Huang B., Zhang Z, & Luo K.Q. (2022). The interactions between integrin α5β1 of liver cancer cells and fibronectin of fibroblasts promote tumor growth and angiogenesis. International Journal of Biological Sciences, 18(13), 5019-5037.

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Quantitative Neuronal Morphometry

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Dendrites and cell body of fluorescent dentate neurons were traced using a computer-controlled microscope-based system (Axio Imager A2 Zeiss microscope, 100X oil-immersion objective) with a software (Neurolucida® software; MicroBrigthField Bioscience) that provides neuron tracing tools to trace from a live camera image (QImaging).
For spine analysis, confocal stacks of images were obtained with a Leica SP5 confocal microscope (63X oil-immersion objective; XY dimensions: 41.0 µm; z-axis interval: 0.13 µm). The dendritic length of each segment was measured on Z projections, and the number of dendritic spines was counted using NeuronStudio software [35 (link)]. Before spine analysis, images were deconvoluted using AutoQuantX3 software (Media Cybernetics). A minimum of 30 dendritic segments per experimental group and time point were examined for spine analysis.
Morphometric analysis of the AIS was done as previously described [36 ] using a Leica SP5 microscope (63X water-immersion objective; XY dimensions: 82.0 µm; z-axis interval: 0.21 µm).

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Zebrafish Neuronal Imaging and Analysis

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The hcrt:EGFP and HuC:GFP zebrafish offspring (n=13/group) born from control-gelatin and ethanol-gelatin consuming females were mounted ventral side at 28 hpf down within 1% low-melting-point agarose containing 15 mM Tricaine Methanesulfonate (Pentair, Cary, NC) within a metal slide with a 15 mm diameter well drilled out from the center and a 24 × 50 × 1 mm glass coverslip adhered to the bottom via high vacuum grease. Following behavioral testing, the same hcrt:EGFP zebrafish at 6 dpf (n=10/group) and 12 dpf (n=16/group) were mounted dorsal side down, and all z-stack images were acquired with an inverted Leica SP5 laser scanning confocal microscope with a 20 x or 40x water immersion lens and 1 μm step size. Deconvolution of confocal images was performed using AutoQuant X3 software (Media Cybernetics), and images were analyzed using Imaris software (Bitplane, Zurich, Switzerland). HuC⁺ and hcrt⁺ neurons were automatically identified by the software using a 6 μm threshold for cell size, and neurons not accounted for by the software were manually added.

Collier A.D., Min S.S., Campbell S.D., Roberts M.Y., Camidge K, & Leibowitz S.F. (2019). Maternal ethanol consumption before paternal fertilization: Stimulation of hypocretin neurogenesis and ethanol intake in zebrafish offspring. Progress in neuro-psychopharmacology & biological psychiatry, 96, 109728.

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