It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
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.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
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.
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.
Provides a toolbox for neuropil decontamination in calcium imaging datasets. FISSA removes several sources of contamination without leading to negative signal artefacts by presenting a standardized and user-independent method. This software process by determining a set of neuropil regions around pre-defined somatic regions of interests (ROI). It utilizes non-negative matrix factorization nuclear magnetic resonance (NMR) to split the signals form these regions.
A version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.