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.
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.
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.
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.
Offers a user interface that automatically generates annotations in a standardised format. AnnoSys provides generalised annotation body structures and generalised robust fragment selection mechanisms and identity management by role based authorization. The implementation of this method is generic for all kinds of biological collection data as well as for species occurrence observation data on all kinds of organisms.
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.