Data management/Annotation software tools | Laser scanning microscopy image analysis
Find and compare the best bioinformatics software tools for navigating, sharing and collaboratively annotating massive image data sets of laser scanning microscopy. Tools are ranked by the biomedical research community.
Explores and annotates large-scale volume data. KNOSSOS is a standalone software that allows user to screen neurites by using three orthogonal views and is able to handle data from serial blockface scanning electron microscopy (SBFSEM). The application provides both a skeletonization and a 3D segmentation mode. The software can also be customized by Python plug-ins as well as be incorporated into external workflows.
Allows to navigate, share and collaboratively annotate massive image data sets of biological specimens. CATMAID combines three main components: a centralized data server, decentralized image servers and the client-side user interface. The interface is applicable to any 2D or 3D multimodal biological image datasets, as shown in examples of stitched confocal 3D volumes. Additionally, the interface can be used to navigate, annotate and bookmark locations in any large image canvas.
An open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. HTML5 PivotViewer provides a powerful method to allow end users to mine their data.
Annotates and screens 3D image data with the aim of easing circuit rebuilding. PyKNOSSOS is a standalone software which provides four working modes: (i) browsing files including a for multi-resolution viewing, (ii) a tracing features that is able to perform manual skeleton tracing, orthogonal tracing and arbitrary reslices; (iii) a tagging module; and (iv) synapse annotation tools. In addition, it includes a feature for visualization by using VTK-Python bindings.
It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. The customizability of BIOCAT is expected to be useful for providing effective and efficient solutions for a variety of biological problems involving image classification and annotation.
It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
Allows users to manage image data, results and derived data, and image analysis protocols. Imaris permits to tag resources as a search across all experiments or a specific set of experimental groups. It contains several features allowing to: (1) visualize volume images and objects, (2) identify objects according to their morphology, intensity, and more, (3) validate segmentation, (4) interact with objects, (5) create pictures and stunning animations.
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.
Investigates heterogeneous genomics and health care data of high volume. PROMIS-Med consists of a web available platform that allows researchers to manage, study and display complex health care information about patients. It can deal with data such as: patient life style, medical history, visits to the practice, wet lab and imaging test, diagnoses, medications, etc. This tool aims to enhance the quality and transition of health care.
Permits creation, edition, and annotation of a collection of globular objects. VANO is a cross-platform 3D annotator that can be used to build a 3D digital nuclei atlas for Caenorhabditis elegans and a 3D digital atlas of the nuclei of the ventral nerve cord of late stage Drosophila melanogaster embryos. This tool also serves for annotating images in contexts where the image objects have an irregular shape or for collecting prior information and statistics of image objects.
Allows users to analyze 3D models from segmentations of electron microscopy (EM) image stacks. NeuroMorph provides an assortment of tools executable through the Blender software that consists of five modules: (i) Measurements tools, (ii) 3D drawing, (iii) Center Lines and Cross Sections, (iv) Proximity Analysis and (v) a toolkit called “Other Tools” that provides additional functionalities for generating image stacks or to import objects. The modules can be downloaded separately or as a complete package.
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