Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Enables users to reconstruct big images/stacks from an arbitrary number of tiled input images/stacks. Stitching is based on the Fourier Shift Theorem, and computes all possible translations between pairs of 3D images. It avoids the propagation of errors by consecutive registration steps. Moreover, this tool uses phase correlation to find the translation between all image pairs and registers multi-tile acquisitions globally minimizing all pairwise registration errors.
Provides general purpose functionality for reading, writing, processing and analysis of images. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization. It uses ImageMagick to read and save images, and supports more than 80 image formats, including JPEG, TIFF, TGA, GIF and PNG. EBImage also supports standard geometric transformations such as rotation, reflection, cropping, translation and resizing. Classical image processing tools are available: linear filtering, morphological erosion and dilation, fast distance map computation, contour delineation and area filling.
Allows users to perform phase correlation registration to correct movement that occurs as a result of sample drift in three-dimensional (3D) time lapse experiments. Correct 3D Drift is a Fiji plug-in assisting in the correction of the sample drift. It compensates for sample translation or alterations in focal position by utilizing phase correlation to register each time-point of a four dimensional (4D) confocal datasets.
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.
Provides methods that combines multiple microscopic recordings. XuvTools is an automated 3D stitching software developed for biomedical image data, typically confocal microscopy images. It permits to obtain a large field of view, a high dynamic range or good resolution. This software does not require a priori information on the stage positions. It is split into core library, command line tools for batch processing and a graphical user interface.
Allows users to implement and assemble control software for custom-built microscope systems. Helio provides a framework, built around a collection of components arrangeable according user needs, which can support multiple hardware and functional combinations. The application is able to handle a wide range of laser-scanning including galvanometric scan mirrors or resonant scanners as well as camera images.