A software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data.
Permits surface rendering, multivariate statistical analysis (MSA), automatic classification, projection matching, angular reconstitution, automatic particle selection. IMAGIC can be employed for real data processing run for educational or testing purposes. This tool can exploit the properties of cheap graphic processors. It is useful for 4D analysis at atomic resolution or for refining towards multiple 3D structures.
Allows to convert metabolomic studies in .mzML and .imzML format to the open ISA-Tab standard. mzML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines. It facilitates more finely grained data exploration and querying of datasets.
A library software to create extensible framework for the reading, writing, and translation of images. SCIFIO was designed to provide the architecture that will equally facilitate: i) the conversion of additional formats into supported open-exchange formats such as OME-TIFF and ii) the integration of additional scientific open-exchange formats. The extensible design of SCIFIO facilitates community contribution, the establishment of domain-specific metadata standards, and integration into a unified system capable of adapting to the demands of scientific imaging analysis.
Converts TRACE files into PostScript format. Trace2PS provides an easy to handle software toolkit implemented in Perl. Due to its platform independency, it can be integrated into a variety of software projects or data analysis pipelines. The user can also supplement the field content by missing trace file items or customize the content by overwriting the default. The PostScript’s output can afterwards be converted into various file formats.
Converts the metadata in proprietary scientific image file formats into the open Open Microscopy Environment (OME) Data Model. OME Files provides a seamless, performant way for these calculations to use OMETIFF. It provides interoperability with the wide range of existing software supporting OME-XML and OME-TIFF formats. The tool is several-fold faster reading and writing metadata from a multi-dimensional fluorescence image. It is a performant, useful resource for reading and writing OME-TIFF in several different use cases.
Converts images, 2-D images and 3-D volumes, from and to formats typically used in 3-D electron microscopy (3DEM). em2em includes an option that permits users to convert stacks of image files in one step. Images from different workstations and commons operating systems can be automatically converted.
Permits to convert proprietary Philips PAR/REC images to neuroimaging informatics technology initiative (NIfTI). dcm2niix is easy to use, offers features to specify output file names. It is suitable for clinical environments. The tool is able to convert diffusion vectors and shows good results for job with Computerized-Tomography (CT) scans. It offers a graphical user interface (GUI) that permits to display an example for how user files will appear. dcm2niix offers a way to save the output to a specific folder or whether the NIfTI images should be created in the same folder as the input DICOM files.
Offers read-only access to the information contained in files in CZI format. libCZI provides several functionalities such as: (1) reading subblocks and get the content as a bitmap; (2) reading subblocks which are compressed with JPEG-XR; (3) works with tiled images and pyramid images; (4) composing multi-channel images with tinting and applying a gradation curve; and (5) giving access to metadata.
Reads and writes data in life sciences image file formats. Bio-Formats is a library developed by the Open Microscopy Environment, that aims to convert proprietary microscopy data into the OME data model, an open standard called. The software can parse both pixels and metadata for a large number of formats, and write to several formats. It can be used as a plugin for ImageJ/Fiji.
Converts from a Zeiss AxioVision TIFF file to one that can be compatible with SoftWoRx software on SGI boxes. ZeissToSGI intends to bypass the inherent problem of processing large image files with silicon graphics image (SGI).
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