Offers a plugin for unusual biological samples mapping. µ-Magellan is an open-source program allowing users to perform high-throughput imaging on various levels of space and time in three dimensions. The application gives users the possibility to alter a wide range of settings including spatial regions or automated excitation calculations and to generate files which can be exported towards many software such as Vaa3D/TeraFly or Imaris.
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.
Serves for stitching of large 2D time-lapse mosaics. MIST can estimate the mechanical stage model parameters from the computed translations to limit the optimization search space. It also minimizes stitching errors by constraining and optimizing the translations within a square area. It can be used on any grid-based dataset like those acquired by a microscope. Moreover, this tool utilizes normalized cross correlations to compute image registrations.
Allows automatic 3D stitching of teravoxel-sized tiled images. TeraStitcher was initially developed for stitching images generated by the confocal laser scanning microscopy (CLSM) microscope. The software specifies the requirements of the stitching problem when teravoxel-sized images are involved, and then use the system resources to perform the stitching of these images. It is available both as standalone application and as plugin of the free software Vaa3D.
Applies a recursive normalization algorithm to stitch large-scale immunofluorescence-based mosaics without incurring vignetting seams. QuickStitch works successfully for tissues of differing size, morphology, and fluorescence intensity. It requires no specific information about the imaging system. It is provided as an open-source tool that is both user friendly and extensible, allowing straightforward incorporation into existing image processing pipelines. This enables studies that require accurate segmentation and analysis of high resolution datasets when parameters of interest include both cellular-level phenomena and larger tissue-level regions of interest.
Reconstructs and makes complex datasets easily accessible. BigStitcher is an ImageJ plugin that enables interactive visualization, precise alignment, real-time fusion, deconvolution, support for alignment of multi-tile acquisition taken from different physical orientations, or so-called multi-tile views. It can also be used for doubling the size of specimens that can be imaged, while further orthogonal views can render the resolution isotropic.
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 visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
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