Curator Dashboard

Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Image processing and analysis software.

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• SciCrunch
• 11 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software used for a variety of functions including image automation frameworks and advanced 3D data quantification, and simulation technologies.

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• SciCrunch
• 11 years ago - by Anonymous

Software designed to record and organize data. All experiments and subject data are entered into a database, with all subject data linked together allowing the software to track everything, and save it based on the assigned Subject ID. All standard data is displayed in real time along with a cumulative plot of the subject’s activity for all chambers. Users may choose the specific chamber size allowing for distance traveled to be measured in real units instead of beams broken. A rotational analysis option allows examination of large or small rotations, allowing for rotational measures to be obtained on staggering, ataxic, lesioned, or other loco-motor impaired mice or rats. Zonal analysis allows the user to change boundaries around the animal in post analysis. Up to eight systems can be connected to one computer.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

A suite of MATLAB/C and C++ tools for computing standard and extended versions of transfer entropy (as recorded by Thomas Schreiber) on sparse, binary time series. Delay 1, delayed, and higher-order transfer entropy are available in the toolbox. The speed of the program is dependent upon the number of delays, the length of the data set, the number of neurons, and the message length/order. Documentation and examples are provided on the website.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software designed for single or multi-wavelength intracellular ion measurements. It provides simultaneous display of raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A desktop application used to create and manage 2D and 3D animation and video and audio assets. SAP Visual Enterprise Author can be used to render visual content into common desktop documents, file formats, and business applications for secure downstream use. A variety of tools allows users to view, transform, optimize, animate, and publish in different formats.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software used for modeling, simulation, and rendering of 3-D models. The tool is designed to provide a starting point to model, animate, work with lighting, and create VFX.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

A protein family specific platform that works closely with the GPCR community to determine the high resolution structure and function of GPCRs. Structures are available in the glutamate, secretin, frizzled/TAS2, adhesion, and rhodopsin branches of the protein phylogenetic tree. Users can access a list of protein structure targets and completed protein structures.

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• SciCrunch
• 11 years ago - submitted by Yueling Li

A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation.

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• SciCrunch
• 11 years ago - by Anonymous

A software tool which provides a means to acquire and analyze time-series data, as well as a direct route to publication quality graphics. It provides a variety of graph styles and automated, extended, and/or customizable analyses.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje