Contents

Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.

The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.

FracLac is for digital image analysis. Use it to measure difficult to describe morphological features.

This project was designed for vectorize and analyze the  blood vessels in the mouse brain.

This plugin requires the definition of seed point detection settings by the user (Semi-automated).

We have developed a novel approach, named DF-Tracing, to tackle this challenge. This method first extracts the neurite signal (foreground) from a noisy image by using anisotropic filtering and automated thresholding. Then, DF-Tracing executes a coupled distance-field (DF) algorithm on the extracted foreground neurite signal and reconstructs the neuron morphology automatically.

While OpenCV was designed for use in full-scale applications and can be used within functionally rich UI frameworks (such as Qt*, WinForms*, or Cocoa*) or without any UI at all, sometimes there it is required to try functionality quickly and visualize the results. This is what the HighGUI module has been designed for.

It provides easy interface to:

The OpenCV CUDA module is a set of classes and functions to utilize CUDA computational capabilities. It is implemented using NVIDIA* CUDA* Runtime API and supports only NVIDIA GPUs. The OpenCV CUDA module includes utility functions, low-level vision primitives, and high-level algorithms.

The module provides biological visual systems models (human visual system and others). It also provides derivated objects that take advantage of those bio-inspired models.

A complete package for fluorescence lifetime analysis implemented as an R package with sample data.

The wound healing tool measures the area of a wound in a time series of images of cellular tissue. The tool will measure the area of the wound, i.e. the area that does not contain tissue, in each image. The segmentation is based on the fact that the image is more homogeneous in the region of the wound as in the region of the tissue. Via the options, one of two methods to detect the empty area, can be selected. The first uses edge detection, the second a variance filter. Holes in the detected tissue are filled using morphological operations.

nctuTW is a "high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information.