Collection

# Install the ultralytics package from PyPI
pip install ultralytics

You can also install ultralytics directly from the Ultralytics GitHub repository. This can be useful if you want the latest development version. Ensure you have the Git command-line tool installed, and then run:

# Install the ultralytics package from GitHub
pip install git+https://github.com/ultralytics/ultralytics.git@main

Aligning Big Brains & Atlases (ABBA) is a set of software components which allows users to register images of thin serial biological tissue sections, cut in any orientation (coronal, sagittal or horizontal) to atlases, usually brain atlases. ABBA is available as a Fiji plugin for performing registration; a QuPath extension is also available and recommended. Typically, a set of serial sections is defined as a QuPath project, that is registered within Fiji. The registration results can then imported back into QuPath for downstream processing (cell detection and classification, cell counting per region, etc.).

Available atlases include the 3D mouse Allen Brain atlas and the Waxholm Space Atlas of the Sprague Dawley Rat Brain. Depending on your installation method, you may also access all BrainGlobe atlases.

SNT is ImageJ’s framework for tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multidimensional microscopy data, semi-automated and automated routines, and options for editing traces. For data analysis, SNT features advanced visualization tools, access to all major morphology databases, and support for whole-brain circuitry data.

VTK is an open-source software system for image processing, 3D graphics, volume rendering and visualization. VTK includes many advanced algorithms (e.g., surface reconstruction, implicit modeling, decimation) and rendering techniques (e.g., hardware-accelerated volume rendering, LOD control).

VTK is used by academicians for teaching and research; by government research institutions such as Los Alamos National Lab in the US or CINECA in Italy; and by many commercial firms who use VTK to build or extend products.

The origin of VTK is with the textbook "The Visualization Toolkit, an Object-Oriented Approach to 3D Graphics" originally published by Prentice Hall and now published by Kitware, Inc. (Third Edition ISBN 1-930934-07-6). VTK has grown (since its initial release in 1994) to a world-wide user base in the commercial, academic, and research communities.

The BioVoxxel Toolbox is a suite which contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. The following plugins are hosted here:

• Extended Particle Analyzer
• Binary Feature Extractor
• Speckle Inspector
• Watershed Irregular Features
• EDM Binary Operations
• Filter Check
• Pseudo flat-field correction
• Convoluted Background Subtraction
• 2D Particle Distribution (Distribution_Analysis)
• Cluster Indicator
• SSIDC Cluster Indicator
• Gaussian weighted Median filter
• Adaptive Filter
• Enhance True Color Contrast
• Mode and Differential Limited Mean Binarization
• Basic Recursive Filter