Segmentation is one of the fundamental digital image processing operations. It is used ubiquitously across all scientific and industrial fields where imaging has become the qualitative observation and quantitative measurement method.
Allows users to manage image data, results and derived data, and image analysis protocols. Imaris permits to tag resources as a search across all experiments or a specific set of experimental groups. It contains several features allowing to: (1) visualize volume images and objects, (2) identify objects according to their morphology, intensity, and more, (3) validate segmentation, (4) interact with objects, (5) create pictures and stunning animations.
A free, open-source system designed for flexible, high-throughput cell image analysis. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
Offers a platform for neurons rebuilding. NeuRA is able to handle image stacks from 2-photon microscopy and to perform their automatic conversion. The application includes a graphic interface allowing users to filter raw data for then segmenting it. Lastly, the software can reconstruct the geometry. It can be used for investigating neuronal plasticity.
A three-dimensional (3D) reconstruction and modeling software. Free-D allows to generate, process and analyze 3D point and surface models from stacks of 2D images. It is an integrated software tool, offering in a single graphical user interface all the functionalities required for 3D modeling.
Segments and studies stacks of image data. Costanza can be very useful for data from fluorescent microscopy. Its aim is the segmentation of nuclei marked cells in three dimensions. This tool returns the result both as cells/intensities marked in images. It employs intensity thresholds that allows for segmentation of data of varying intensity. This module gives to users 3D median filter as an optional noise reduction processor.
Allows users to detect and count fluorescent signals in microscopy images of cells. Blob Finder is a free software that performs two types of analysis: (i) an average count, for quantifying the number of nuclei and signals in an image; (ii) and a single cell analysis, that assigns each signal to the closest cell and get a signal count for each cell in the image. It also performs on-z_stacks of the cell with a maximum projection to project the image data into a 2D image.