Performs crowd-based images annotation. Quanti.us is a portal that assists users in recruiting groups of untrained Mechanical Turk workers (Turkers) to annotate images using a set of interaction tools. The platform enables uploading of image sets, selection of an analysis tool, and provides sets of instructions. Users can gather hand annotations by marshaling paid Turkers to annotate a range of image types. Quanti.us thus makes crowd analysis of scientific images applicable to several annotation problems.
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 wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. SpotCaliper is able to automatically find spots of varying size, and gives a precise measurement on their radius. The detections are collected in a table, displaying the following parameters: unique identifier (ID) of the spot, its location (x and y coordinates), radius, confidence, contrast, SNR and type. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way.
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.
Discovers the “classical” endpoints neuron quantification and neuronal morphology but also novel endpoints like radial migration and neuronal density distributions within the Neurosphere Assay. Omnisphero aims to automated high-content image analysis (HCA) developmental neurotoxicity (DNT) screenings. It can be applied in other 3D in vitro systems such as in the migration assay of tumor spheroids.
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.
A free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging. TLA is a graphical tool which enables easy access to high-throughput live cell imaging for every user, regardless of the individual expertise. Beginners can easily process stacks of time-lapse data by loading an appropriate image processing setup and time-lapse evaluation setup. Advanced users can modify existing setups, or create new setups which suit their need and special experimental conditions.
A tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying: 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma and 4) the complexity and extension of neurons.
Provides assistance for the analysis of high-throughput microscopy-based screens. imageHTS main features are segmentation of cells, extraction of quantitative cell features, prediction of cell types and visualization of data through web interface. This software offers a standardized access to remote screen data to facilitate the dissemination of high-throughput microscopy-based screens.
Executes automated batch analysis of JPEG images of aniline-blue stained callose deposits. AutoSPOTs identifies and quantifies fluorescent spots on JPEG files. Users can configure filter settings for average sensitivity and accuracy in enumeration of callose deposits. This software offers features such as color filtering, multiple pixels selecting, values recording or average measuring.
Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of applications such as cell/nuclei counting, cell/nuclei tracking, 3D neuron detection and analysis, machine learning cell classification, particle tracking, wound healing and calcium oscillation tracking. Aivia also comes with editing tools to help get even better results.
Permits scientific evaluation of 2D images. GSA Image Analyser is a program that allows (1) automatic surface calculation of the surfaces of all recognized objects, (2) direct length calculation of very complex and very ramified objects, and (3) object counting with an automatic count-function, a grid-intersection-count-function and two manual count-procedures.
Assists in quantification of zebrafish neuronal cells. This tool consists in four stages: (1) it produces a diffused gradient vector field; (2) it calculates a response image; (3) it performs non-maximum suppression on the response image and spots detection candidates; (4) and it groups the detected objects into clusters based on their color information. This tool can be applied to different data samples such as cell death detection, immunohistochemistry, and nuclear staining.
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