Provides assistance for elastic volume reconstruction via series of ultra-thin microscopy sections. Elastic Alignment and Montage works for the ImageJ software through the TrakEM2 toolkit. This elastic alignment method is appropriate for groups of overlapping 2D-images. It enables the montage of mosaics from overlapping tiles and the alignment of deformed section series from serially sectioned volumes.
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.
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 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.
Estimates the positions and spacing between sections (or at local points) of three dimensional image data. Z-Spacing is an image-based method for the correction of continuous and discontinuous non-planar axial distortions in serial section microscopy. It may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. It also provides plugins for both Fiji and TrakEM2.
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