A retrospective illumination correction method for optical microscopy. CIDRE is designed to correct collections of images by building a model of the illumination distortion directly from the image data. Larger image collections provide more robust corrections. CIDRE achieves correction quality similar to that of prospective methods. Unlike existing retrospective methods, CIDRE estimates both linear intensity gain function and an additive term. The key insight to our approach is that the distribution of intensities from a single location across many images is related to an underlying distribution common to all locations by a linear transform. This assumes that objects may appear anywhere in the image with equal probability.
Analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution. By using a hidden Markov model (HMM), 3b allows useful information to be obtained from data that would be impossible to analyse with standard localisation analysis techniques.
Characterizes scientific complementary metal-oxide semiconductor (sCMOS)-specific noise in each pixel and incorporates the noise statistics in the likelihood function for single-molecule localization. NCS corrects pixel-dependent noise in fluorescence microscopy using an sCMOS sensor. It can be applied to sCMOS-based detection and quantitative analysis in a broad spectrum of microscopy techniques.
Finds dynamic changes in pixel intensity between image frames. MUSCLEMOTION expresses the output as a relative measure of movement during muscle contraction and relaxation. It can be employed for multiparameter recording conditions and experimental settings using transmitted light microscopy, fluorescent membrane labeling, fluorescent beads embedded in soft substrates or patch clamp video recordings.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Serves for vector-valued image regularization. Anisotropic Diffusion 2D is a program based on variational methods and partial differential equations (PDEs). This tool consists in a single generic anisotropic diffusion equation that provides a simple interpretation of the regularization process in terms of local filtering with spatially adaptive Gaussian kernels. It also offers the possibility to specialize a generic expression into different regularization PDEs depending on different applications: flow visualization, image restoration, magnification, or inpainting.
Investigates fungal area extension. HyphaTracker is a module, executable through ImageJ, able to handle germinating fungal spores study. The application includes features to eliminate targeted particles or crossing hyphae during analysis and to perform a semi-automatic image processing of multiple germlings per field of view. This program can be applied to other fungi species with additional modification.
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.
A 4-D image processing platform for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software.
Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.
Balances jittery image stacks. Image Stabilizer is based on the Lucas-Kanade algorithm. It can be applied to grayscale and color images. This tool can determine the geometrical transformation needed to best align each of the other slices with the "template".
Allows to visualize and present your images in several dimensions. The functionality of this imaging toolbox expands constantly with a wide range of different modules that are tailored to specific applications or microscope accessories. AxioVision offers countless functions for applications in the field of biological and medical routine research.
Increases the local contrast of an image. CLAHE uses the contrast limited adaptive histogram equalization to process. The contrast amplification in the vicinity of a given pixel value is delivered by the slope of the transformation function. This ImageJ plugin has three main parameters: block size, histogram and max slope.
Serves for iterative image deblurring. PID allows users to deconvolve a color image by splitting the channels and deblur each channel separately. It contains a graphical user interface (GUI) permitting users to specify several types of details such as stopping tolerance, threshold, or log convergence.
Automates image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 tissue sections. ImmunoRatio uses monoclonal antibodis 6F11, PgR636 and MIB-1 to detect respectively ER, PR and Ki-67. It is able to make blank field correction thank to the utilization of the Calculator Plus plugin. The tool segments the DAB- and hematoxylin-stained nuclei areas from a microscope image, calculates the labeling index, and generates a pseudo-colored result image matching of the segmentation.
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