| Variational algorithms to remove stationary noise |
21 |
|
2D, 3D |
|
Software |
… Application to microscopy imaging. This plugin allows to denoise images degraded with stationary noise. Stationary … this plugin are: - Standard white noise denoising using a total variation and fidelity term minimization. Even though total … |
| PureDenoise |
9.782 |
|
3D, multi-channel, time-series |
ImageJ |
Software |
… - 10:55 Download Page http://bigwww.epfl.ch/algorithms/denoise/ Documentation Link http://bigwww.epfl.ch/algorithms/denoise/ Usage Example Link http://bigwww.epfl.ch/algorithms/denoise/ … migration.tool … Florian Luisier … 4147 … 4155 … … |
| SURE-LET Wavelet Denoising |
8 |
|
2D, multi-channel |
MATLAB |
Software |
|
| ImageJ Plugin for Non-Local-Means Filtering |
7.974 |
|
2D |
ImageJ |
Software |
… - 14:38 Download Page https://imagej.net/Non_Local_Means_Denoise Documentation Link https://imagej.net/Non_Local_Means_Denoise Reference Publication Link A Non-Local Algorithm for … |
| Stochastic Denoising |
7 |
|
2D |
ImageJ |
Software |
|
| Image denoising using Matlab |
6 |
|
2D, 3D, time-series |
MATLAB |
Software |
|
| CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji |
5 |
|
2D, 3D, multi-channel |
Fiji |
Software |
|
| BiaPy: Bioimage analysis pipelines in Python |
5 |
|
2D, 3D |
Python |
Software |
|
| nd-safir |
5 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
| BM3D denoising |
5 |
|
|
|
Software |
|
| CAREless |
4.816 |
|
2D, 3D, multi-channel, time-series |
ImageJ, Python |
Software |
|
| Kalman Stack Filter (ImageJ) |
3 |
|
2D |
ImageJ |
Software |
|
| Super-Resolution Radial Fluctuations (SRRF) |
3 |
|
2D, time-series |
ImageJ |
Software |
|
| APEER |
3 |
|
|
|
Software |
|
| KNIME Average Filter |
3 |
|
|
KNIME |
Software |
|
| KNIME Anisotropic Diffusion |
3 |
|
|
|
Software |
|
| CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Knime |
3 |
|
|
KNIME |
Software |
|
| BioImage Model Zoo |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
| DeepImageJ |
3 |
|
|
ImageJ, Tensorflow |
Software |
|
| Sigma Filter |
3 |
|
2D |
ImageJ |
Software |
|
| MorphoGraphX |
3 |
|
3D, multi-channel |
|
Software |
|
| clij2 |
3 |
|
2D, 3D |
Fiji, Icy, MATLAB |
Software |
|
| Filter Toolbox (Icy) |
3 |
|
2D |
Icy, EzPlug SDK, Icy Protocols SDK |
Software |
|
| ZeroCostDL4Mic |
3 |
|
2D, 3D |
|
Software |
|
| Relate |
2.969 |
|
2D, 3D, multi-channel |
|
Software |
|
| VIGRA |
2.563 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… non-linear diffusion (adaptive filters), hourglass filter total-variation filtering and denoising (standard, higer-order, and … non-linear diffusion (adaptive filters), hourglass filter total-variation filtering and denoising (standard, … |
| Manual Tracking Components of ImageJ |
2 |
|
2D, time-series |
Fiji |
Software |
|
| Generalized Riesz-Wavelet Toolbox for Matlab |
2 |
|
2D |
MATLAB |
Software |
|
| Qupath Multiplex Analysis |
2 |
|
|
|
Software |
… of positive markers. The workflow also adds the total numbers of positive cells for each marker to the … of positive markers. The workflow also adds the total numbers of positive cells for each marker to the … |
| ICY batch pixel density measurement |
2 |
|
2D |
|
Software |
… the ratio of pixels over a given threshold over the total number of pixels in the ROI. has function Object … the ratio of pixels over a given threshold over the total number of pixels in the ROI. … ICY batch pixel density … |
| TrackMate |
2 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… or yield further analysis results such as velocity, total displacement, diffusion characteristics, division … or yield further analysis results such as velocity, total displacement, diffusion characteristics, division … |
| MicrotubuleTracker in FIJI |
2 |
|
2D, 3D, time-series |
Fiji |
Software |
… of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such … of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such … |
| ImmunoRatio |
2 |
|
2D |
ImageJ, Colour Deconvolution |
Software |
… the primary measurement made is percentage of the total nuclear area , not the percentage of detected nuclei … the primary measurement made is percentage of the total nuclear area , not the percentage of detected nuclei … |
| AnaMorf |
2 |
|
2D, multi-channel, time-series |
ImageJ |
Software |
… using the descriptors projected area, circularity, total hyphal length, number of hyphal tips, hyphal growth … using the descriptors projected area, circularity, total hyphal length, number of hyphal tips, hyphal growth … |
| MosaicSuite |
2 |
|
2D, 3D, time-series |
Fiji, ImageJ 2.x |
Software |
|
| Temporal Medial Filter |
2 |
|
2D, time-series |
|
Software |
… than time taken for a feature to traverse a pixel (NB. total window is 2x half-width +1) moving foreground … than time taken for a feature to traverse a pixel (NB. total window is 2x half-width +1) moving foreground … |
| Cell or particle counting and scoring the percentage of stained objects |
2 |
|
2D, multi-channel |
CellProfiler |
Software |
… object inside only. The percentage of positive nuclei vs total number of nuclei can then be computed using the … object inside only. The percentage of positive nuclei vs total number of nuclei can then be computed using the … |
| DeconvolutionLab2 |
2 |
|
3D |
ImageJ |
Software |
… Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative … Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), … |
| Spimagine |
2 |
|
3D, time-series |
OpenCL |
Software |
|
| nanoFeatures |
2 |
|
2D, multi-channel |
Matlab Image Processing Toolbox, Matlab Computer Vision System Toolbox, MATLAB |
Software |
… aspect ratio, and number of localizations per cluster (total and for each channel). has function Operation Analysis … aspect ratio, and number of localizations per cluster (total and for each channel). … nanoFeatures … |
| Mean shift |
2 |
|
|
|
Software |
|
| QuantiFish |
2 |
|
2D |
|
Software |
… and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also … and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also … |
| BaSiC |
2 |
|
2D, time-series |
Fiji |
Software |
… to solve both shading in space and background variation in time. It can correct temporal drift in … to solve both shading in space and background variation in time. It can correct temporal drift in … |
| Microtubules Tool (3D) |
2 |
|
3D, multi-channel |
ImageJ, Fiji, Skeletonize3D, 3D Objects Counter |
Software |
… source License CeCILL-C Description The tool measures the total length of the microtubules in a 3D image. See: … … Bioimage informatics … The tool measures the total length of the microtubules in a 3D image. See: … |
| Focal Adhesion Analysis Server |
1.969 |
|
|
|
Software |
… Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). … has biological terms Focal Adhesion Additional keywords Total Internal Reflection Microscopy Entry Curator migration … Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). … |
| QuimP |
1.733 |
|
2D, multi-channel, time-series |
|
Software |
… employed, but usually fail to meet the requirement that total fluorescence must not change. QuimP uses a method … employed, but usually fail to meet the requirement that total fluorescence must not change. QuimP uses a method … |
| ImageM |
1 |
|
2D, 3D |
Matlab Image Processing Toolbox, MATLAB, MATLAB Statistics toolbox |
Software |
|
| Aivia - Aivia Cloud - Aivia Web |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
| TTK the Topology Toolkit |
1 |
|
3D |
Paraview |
Software |
|
| Distance Analysis (DiAna) |
1 |
|
2D, 3D, multi-channel |
Fiji |
Software |
… of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based … of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based … |
| ANTs: Advanced Normalization Tools |
1 |
|
2D, 3D, multi-channel |
ITK |
Software |
|
| Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ) |
1 |
|
3D |
ImageJ |
Software |
|
| Nuclei Segmentation (Python) |
1 |
|
2D |
scikit-image, SciPy, NumPy |
Software |
|
| Nuclei Tracking (ImageJ) |
1 |
|
3D, time-series |
ImageJ |
Software |
|
| Data-analysis strategies for image-based cell profiling |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
| OpenCV / Computational Photography |
1 |
|
|
OpenCV |
Software |
|
| PixFRET |
1 |
|
2D |
ImageJ |
Software |
|
| SLOTH |
1 |
|
2D, time-series |
SciPy, NumPy, Python, matplotlib |
Software |
… microtubules tubulin cytoskeleton Additional keywords Total Internal Reflection Microscopy Entry Curator kota Post … |
| MeasureNeurons (CellProfiler) |
1 |
|
2D |
CellProfiler |
Software |
… files are available in the discussion. Measure Neurons - Total Neuron Length Measurement has function Neuron image … files are available in the discussion. Measure Neurons - Total Neuron Length Measurement … MeasureNeurons … |
