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The Holistic Ape Group

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Matlab 7.0 Software ((NEW)) Free 19

The RIT Digital Den store offers educational pricing on selected software. Please note that the prices in the Digital Den are typically for shrinkwrapped copies of software (suitable for sale to individuals), and may not reflect the full discount that RIT departments can achieve. For more information, contact the RIT Digital Den store at 475-2501.

matlab 7.0 software free 19

RIT has had campus-wide software licensing and maintenance coverage for Mac OS operating systems for RIT-owned computers since 2002. Certain Apple software is also available to be installed on RIT-owned computers without extra charge. For instructions on installing this software, please click here.

Departments and faculty can use AutoDesk software products, including AutoCAD for Academic use for free. For more information contact the RIT Service Center. Students can download 13-month versions of the software at the Autodesk Student Community. To sign up, visit -software/overview?sorting=featured&page=1.

ESRI designs and develops the worlds leading geographic information system (GIS) technology. Its leading product - ArcGIS - is a powerful tool that can be used to analyze a wide variety of data against geographic information. Various colleges at RIT participate in the cost sharing of the license for RIT. If you are interested in joining or already participate and need access to the software, contact the RIT Service Center. For more information about ESRI, refer to

Predictive analytics software for scientists and engineersAs the pro version of JMP statistical discovery software, JMP Pro goes to the next level by offering all the capabilities of JMP plus advanced features for more sophisticated analysis including predictive modeling and cross-validation techniques. Users can harness the power and speed of the supercomputer on their desk to explore and understand data in an easy-to-use interface.

MATLAB is a programming platform used to analyze data, develop algorithms, and create models and applications. RIT has a licensing agreement with MathWorks to provide faculty, staff and students with access to many products in the MATLAB suite. The software is available for Windows, macOS, and Linux. RIT's contract covers a selection of Standard and Additional Toolboxes.

CAMPUS is a three year licensing agreement that RIT has secured with Microsoft to provide Faculty and Staff the ability to keep Microsoft Windows and Microsoft Office up do date on both their work and home computers. This agreement applies only to MS Windows and MS Office. Other software, such as Microsoft Windows Server, is covered by the SELECT agreement described below.

SELECT is a three year volume purchasing agreement that allows RIT to purchase a number of different Microsoft software titles at a substantial discount from standard retail or other special academic pricing, and also allows licenses and media to be purchased separately.

NOTE: The SELECT agreeement does not allow unlimited installation or concurrent use of any software. All licenses granted under SELECT are for a specific number of installations on specific machines, and must be paid for with an RIT Purchase Order.

Several departments are sharing a campus license for Minitab and Minitab Express to be used on RIT-owned computers. Minitab is a Windows-only application where as Minitab Express is available for Windows and Mac. To get Minitab or Minitab Express for your RIT Owned computer, please contact your Systems Administrator. Minitab and Minitab Express are also available for use by all current students and faculty on their personal computer for academic purposes. For more information and to download the software, visit our Minitab download page (student or faculty login required).

Histological assessment of skeletal muscle tissue is commonly applied to many areas of skeletal muscle physiological research. Histological parameters including fiber distribution, fiber type, centrally nucleated fibers, and capillary density are all frequently quantified measures of skeletal muscle. These parameters reflect functional properties of muscle and undergo adaptation in many muscle diseases and injuries. While standard operating procedures have been developed to guide analysis of many of these parameters, the software to freely, efficiently, and consistently analyze them is not readily available. In order to provide this service to the muscle research community we developed an open source MATLAB script to analyze immunofluorescent muscle sections incorporating user controls for muscle histological analysis.

The software consists of multiple functions designed to provide tools for the analysis selected. Initial segmentation and fiber filter functions segment the image and remove non-fiber elements based on user-defined parameters to create a fiber mask. Establishing parameters set by the user, the software outputs data on fiber size and type, centrally nucleated fibers, and other structures. These functions were evaluated on stained soleus muscle sections from 1-year-old wild-type and mdx mice, a model of Duchenne muscular dystrophy. In accordance with previously published data, fiber size was not different between groups, but mdx muscles had much higher fiber size variability. The mdx muscle had a significantly greater proportion of type I fibers, but type I fibers did not change in size relative to type II fibers. Centrally nucleated fibers were highly prevalent in mdx muscle and were significantly larger than peripherally nucleated fibers.

The MATLAB code described and provided along with this manuscript is designed for image processing of skeletal muscle immunofluorescent histological sections. The program allows for semi-automated fiber detection along with user correction. The output of the code provides data in accordance with established standards of practice. The results of the program have been validated using a small set of wild-type and mdx muscle sections. This program is the first freely available and open source image processing program designed to automate analysis of skeletal muscle histological sections.

Skeletal muscle has a robust ability to adapt to the pattern of use and to regenerate following injury. These are often quantified using histological techniques. However, the methods for this quantification remain disparate among investigators and often require painstaking manual procedures [1, 2]. The goal of this work is to provide a widely available image processing software package specifically designed for muscle histological analysis.

Altering muscle fiber size is one of the primary methods in which muscle responds to external stimuli. Muscle mass may be increased in response to resistance training [3] or with potential pharmacological agents like myostatin inhibitors [4], while muscle atrophy occurs in response to disuse [5] and injuries such as denervation [6]. These conditions primarily reflect hypertrophy or atrophy of individual fibers rather than hyper- or hypoplasia [7]. Muscle fiber size is routinely evaluated using fixed or frozen tissue sections. Fiber outlines are visualized using a variety of techniques, including hematoxylin and eosin staining, laminin immunostaining, dystrophin immunostaining, and wheat germ aggluttinin staining [8]. While these techniques enable visualization of fiber boundaries, determining fiber cross-sectional area (CSA) is often still performed by manual tracing of individual fibers. There are software programs available to help automate fiber detection, however they are often expensive and are not specifically designed for muscle histology [9].

All of the methods discussed above are commonly performed using immunofluorescence, which provides high contrast in stained and unstained structures. We have developed MATLAB (MATLAB and Image Processing Toolbox 2014a, MathWorks) scripts bundled into a MATLAB App (see Availability and Requirements) that automate, or partially automate determination of fiber size, fiber type, centrally nucleated fibers, and capillary density. These programs are created to comply with standard operating procedures developed by TREAT-NMD when available using sophisticated boundary detection algorithms [2]. The software also includes built-in image editing to manually inspect and manipulate fiber boundaries. Fully automated fiber size determination as well as fiber types and CNFs may be possible with adequate image acquisition [9, 20]. However, these newly designed fully automated programs are not yet available [9] and/or have a significant cost [20]. Additionally, allowing the user to have manual control over some aspect of image processing allows users to maintain the fidelity established by manual techniques. The open nature of this software also allows custom usage and further advancement of the methods. For users that do not have access to a MATLAB license or the image processing toolbox we have compiled an .exe file that runs using the freely available MATLAB Runtime Compiler (MCR) version 8.3 ( ). Automating a large portion of muscle histology makes it feasible to analyze full muscle cross-sections, eliminating variability introduced by selecting only a portion of the cross section for analysis. This software is validated with muscles from mdx mice, which have many alterations of muscle fiber morphology compared to wild-type mice [21]. The purpose of this study is to develop freely available automatic and standardized image segmentation platform and validate the program using standard muscle histological analysis.

The software has built in several steps of image processing tools within the same script. Initially the user must select an image file (.bmp, .jpg, .png, and .tif.) to be processed. Following selection of the appropriate file the user is provided a list of the built in functions (Figure 1A). A representative image of a soleus muscle from a 1-year-old mdx mouse is used which has been immunostained with laminin (red) and slow myosin heavy chain (green) as well as DAPI (blue) (Figure 1B and C). Dystrophic muscle can be more difficult to process automatically due greater interstitial spaces and the examples highlight some manual adjustments that may be required. The software includes an Excel (Microsoft) file containing default parameter values (Table 1), which may be altered to the needs of the user. The details of each parameter are discussed in the relevant section below.


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