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BioImageXD
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.
Palm3d / Photoactivated localization microscopy 3D
Turns raw photo-activated localization microscopy data into three-dimensional super-resolved images. Palm3d is a data-processing program that processes in 6 steps: (i) construct a calibration stack; (ii) identify candidate particles in each data image; (iii) localize each candidate particle using the calibration stack; (iv) correct for drift; (v) optionally, link localizations and re-localize and (vi) construct image histograms from localization data.
PALMsiever
Provides a user-friendly means of visualizing, filtering and analyzing localization microscopy (LM) data. PALMsiever includes drift correction, clustering, intelligent line profiles, many rendering algorithms, and 3D data visualization. It incorporates the main analysis and data processing modalities used by experts in the field, as well as several new features we developed, and makes them broadly accessible. It can easily be extended via plugins and is provided as free of charge open-source software.
calcFD
Calculates the fractal dimensionality of a 3D structure. calcFD is designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes. The toolbox includes options to use different masking files and is implemented to use either the box-counting or dilation algorithms and to use either the filled volume or just the surface of the structure. The toolbox can easily be run on all of the participants in a FreeSurfer subject folder, or just on specified subject folders. The Matlab toolbox also includes several functions designed to improve functionality, such as the automatic ‘cropping’ of the volume space to the smallest bounding box necessary to contain the volume, improving computation time drastically. Example files are also provided to aid in using the toolbox for the user‘s needs.
VirusMapper
Creates super-resolution (SR) models of virus nanoarchitecture. VirusMapper assists users in detecting, segmenting, aligning, classifying and averaging large datasets of individual viruses. It can resolve nanoscale changes in virus architecture and can be applied to multiple super-resolution modalities. This tool supports data such as structured illumination microscopy (SIM) or high-quality single-molecule localization microscopy (SMLM) with the requested labelling and localization density. It can be executed through ImageJ or Fiji and is part of the NanoJ project.
MUMDesignTool / MUltifocal plane Microscopy Design Tool
Calculates and plots the practical localization accuracy measure (PLAM). MUMDesignTool offers a user-friendly framework for finding the appropriate number of planes and plane spacings for a multifocal plane microscopy (MUM) setup. It also provides two working modes called “rapid” (noise-free) and “precise” (corrupted by background, stochastic signal amplification and readout noise). This application is capable of exporting the results and acquisition parameters as image and text files.
SparseTracer
A pipeline for the reconstruction of discontinuous neuronal morphology in noisy images. SparseTracer is based on two methods. One is the region-to-region connection (RRC) method for detecting the initial part of a neurite, which can effectively gather local cues, i.e., avoid the whole image analysis, and thus boosts the efficacy of computation. The other is constrained principal curves method for completing the neurite reconstruction, which uses the past reconstruction information of a neurite for current reconstruction and thus can be suitable for tracing discontinuous neurites. SparseTracer is able to deal with the large-scale image dataset.
SmartTracing
An automatic tracing framework for neuron reconstruction that does not require substantial human intervention. SmartTracing algorithm has been implemented as a plugin of Vaa3D, which is the common platform to implement algorithms for the BigNeuron project bench-testing. SmartTracing does not require human input of training exemplars and can self-adapt to different types of neuroimage data. Additionally, the method can be applied to improve the performance of other existing tracing methods.
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.
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