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Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Provides an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. PHOELIX was developed to provide a time-efficient and semi-automated method. The procedures which are part of PHOELIX are drawn from the original MRC helical processing suite with extensions principally developed using the SUPRIM image processing package. The package has been optimized for the processing of actomyosin filaments but has been modified and applied to other helical structures.
Represents a deep learning method for segmenting 3D anisotropic brain electron microscopy images. DeepEM3D can efficiently build feature representation and incorporate sufficient multi-scale contextual information. DeepEM3D is able to produce highly accurate 3D neurite boundary probability maps, thereby requiring only a simple watershed method to do segmentation. This tool uses the power of inception and residual structures in the bottom-up path to integrate image information, and combines skip connection techniques with pyramid multi-scale contexture aggregation in the top-down path.
A deep neural network model architecture that is highly optimized for serial-section transmitted electron microscopy image segmentation. We trained a pixel classifier that operates on raw pixel intensities with no preprocessing to generate probability values for each pixel being a membrane or not. While the use of neural networks in image segmentation is not completely new, we developed novel insights and model architectures that allow us to achieve superior performance on EM image segmentation tasks. Our submission based on these insights to the 2D EM Image Segmentation Challenge achieved the best performance consistently across all the three evaluation metrics.
TEMPy / Template and EM comparison using PYthon
Assists users in evaluating density fits in electron microscopy (EM) reconstructions. TEMPy is a modular library that offers multiple features such as: (i) multiple scores for the comparison, (ii) fits evaluations, (iii) methods for single-fit assessment, (iv) ensemble generation of fits, (v) clustering, and (v) scoring including multiple and consensus ones and (vi) plots for visualization. The application can be integrated into pipelines or software suites.
VAST / Volume Annotation and Segmentation Tool
Allows manual annotation and segmentation of large volumetric (voxel) data sets. VAST is a software which enables to work with voxel data sets in the Terabyte or even Petabyte range at interactive speeds, to explore them visually and to label structures of interest by voxel painting. It can be used to generate volumetric training data sets, and can to some extent also be used for importing, proof-reading and correcting results of segmentation algorithms.
Amira 3D Software for Life Sciences
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.
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.
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