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.
Counts worms, especially in a context of chemotaxis. WormCounter offers to users the possibility to choose image processing or manual inspection. Image processing enables batch analysis of multiple well or plate images. Manual inspection allows users to review the result of image analysis and adjusts errors in fully automated analysis. This module is part of the QuantWorm software.
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.
Analyzes C. elegans lifespan, locomotion, body size, and egg laying assay phenotypes. QuantWorm contains several components for image acquisition and image analysis that provides multiple measurements on C. elegans. This software can be easily modified by developers to adapt methods from several popular systems. It can be used with a microscope equipped with a digital camera and motorized stage.
Allows researchers to obtain mosaics of partially overlapped images. MicroMos is a program containing features for stitching several types of images such as microscopy images. The software is designed to supply visually pleasant mosaics, not suitable for quantitative analyses. It aims to construct mosaics of images acquired with non-automated light microscopes and is based on visual information only. The mosaics are built by incrementally stitching couples of images.
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.
Enables interactive measurements and discoveries over very large images. WIPP is an online application that provides functionality for uploading a collection of image tiles and processing them into calibrated, stitched, and segmented images. Moreover, it can produce a hierarchical pyramid representation with a Deep Zoom visualization and on-demand processing of gigapixel images.
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