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 quantitative detection of membrane compartments at subcellular resolution in intact epidermal tissue. Endosome Detection is a method using quantitative confocal laser microscopy (QCLM) to reveal stress adjustment of membrane trafficking in living Arabidopsis whole-leaf tissue. It enables handling of large sample sets at high-throughput and automated image analysis recording multiparametric quantitative values.
Allows users to automatically count mitotic cells, neurons and glia. DeadEasy caspase is a program that identifies cells based on a combination of pixel intensity and minimum volume in 3D. This tool is designed as an ImageJ plug-in and can be used for analyzing cell survival and cell death in development and in disease, such as neurodegenerative diseases and ageing.
Assists users to count automatically the number of mitotic cells labelled with anti-phospho-histone H3 and of glial cells labelled with anti-Repo in Drosophila embryos. DeadEasy Mito-Glia is a program that can quantify cells labelled with other nuclear markers. It can be used to compare cell counts between large samples of wild-type and mutant specimens, to infer gene function.
Allows analysis of a range of parameters measured in 3D cell culture based on 2D images. PCaAnalyser is an automated image-analysis based software developed as an ImageJ plugin. The software enables high-throughput analysis of images acquired from cells grown in a 3D matrix. It is able to reproducibly analyze immuno-staining of different markers known to be involved in cancer progression including CXCR4, α6 and β1 integrin subunits.
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.
Automates analysis of neuronal morphologies in immuno-fluorescence images. SynD intends to assist users in quantifying dendrite and synapse characteristics. The application performs successively the detection of soma, neurites, and synapses. It can be used to enable the simultaneous analysis of multiple morphological features and permits the screening of genetic and pharmacological treatments.
Performs interactive segmentation and investigation of 3D+t microscopy datasets containing cell boundary information. CellECT allows users to add, delete, or modify segments. It offers an adaptive confidence metric assisting users in the recognition of areas of uncertain segmentation. This tool enables the detection of spurious boundaries and can suggest corrections. Moreover, it can be useful for assessing the quality of segmentations and the efficiency of the available metrics.
Identifies cells, and produces a stack of images with the same number of images as the original raw stack, where the identified cells are reproduced in corresponding locations. DeadEasy Larval Glia permits users to count automatically glial cells labelled with anti-Repo in the Drosophila larval nervous system (VNC). Moreover, this tool can also be used for any other nuclear markers in larval tissues so long as the nuclei are not too close together.
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.
Allows users to count the number of neurons stained with antiHB9 antibodies in Drosophila embryos. DeadEasy neurons is an image processing and object recognition method that detects neuronal nuclei labeled with HB9 over background from a stack of confocal images. Moreover, this tool is designed to automatically count the neurons in 3D.
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.
Offers a method dedicated to the quantification of lipid droplets in 3D stacks. Lipid Droplet Counter is a package, that can be run through the ImageJ software, that is composed of an assortment of plugins allowing users to perform a 3D-bandpass on the targeted stack, and then detects the local maxima and grows regions around them to finally use a segment analyzer to decide, by thresholding, which regions includes a droplet.
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.
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.
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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