| 3D Nuclei Clustering Tool |
14.926 |
|
3D, multi-channel |
ImageJ |
Software |
… License MIT Description Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a … |
| Nuclei Segmentation (Cellpose) |
14 |
|
2D |
|
Software |
… a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It performs 2D nuclei segmentation … |
| Cell or particle counting and scoring the percentage of stained objects |
13.977 |
|
2D, multi-channel |
CellProfiler |
Software |
… the IdentifyPrimaryObject module of CellProfiler to detect nuclei from a channel (e.g DAPI), then again the same module … probe (e.g some particular histone) . Then objects (nuclei) are related to the second object (Histone), to create a parent child-relation ship: where nuclei can have histone has child. Nuclei are then filtered … |
| Nuclei Segmentation (CellProfiler) |
13 |
|
2D |
CellProfiler |
Software |
… a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for … |
| Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ) |
10 |
|
3D |
ImageJ |
Software |
… Free and open source Description The macro will segment nuclei and separate clustered nuclei in a 3D image using a distance transform watershed. As … Object counting Download Page Neubias BIAFLOWS workflow of nuclei segmentation 3D with ImageJ has comparison BIAFLOWS … |
| Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ) |
9 |
|
2D, 3D |
ImageJ |
Software |
… Free and open source Description The macro will segment nuclei and separate clustered nuclei in a 3D image using a 2D Gaussian blur, followed by … has topic Bioimage informatics has biological terms nuclei nucleus Entry Curator czhang Post date 01/23/2020 - … |
| Nuclei Segmentation (Python) |
9 |
|
2D |
scikit-image, SciPy, NumPy |
Software |
… This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected. has function Adaptative thresholding … Object detection Smoothing has biological terms nuclei nucleus Entry Curator lascholz Post date 02/26/2019 - … |
| Nuclei Segmentation 2D (ImageJ) |
8 |
|
2D |
ImageJ |
Software |
… Free and open source Description The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask … extraction Download Page Neubias BIAFLOWS workflow of nuclei segmentation with ImageJ has comparison BIAFLOWS … |
| Nuclei Segmentation (ilastik) |
7 |
|
2D |
ilastik, scikit-image, SciPy, NumPy |
Software |
… Free and open source Description NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python … has topic Machine learning has biological terms nucleus nuclei Additional keywords probability map Entry Curator … segmentation Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation with Ilastik and Python Reference … |
| Nuclei Segmentation 3D (NucleiSegmentation3D-ilastik) |
7 |
|
3D |
ilastik |
Software |
… License/Openness Free and open source Description Execute Nuclei Segmentation in 3D images using pixel classification … - 13:26 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ilastik Reference Publication … learning for (bio)image analysis has comparison BIAFLOWS NUCLEI-SEGMENTATION-3D … lascholz … Paavolainen, Lassi … 4073 … |
| Nuclei Segmentation (Mask-RCNN) |
6 |
|
2D |
|
Software |
… Free and open source Description NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses … - 17:10 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation with Mask-RCNN Documentation Link Mask … segmentation on Keras… has comparison Neubias BIAFLOWS Nuclei Segmentation Project … lascholz … Paavolainen, Lassi … … |
| Nuclei Segmentation (DeepCell) |
6 |
|
2D |
scikit-image, SciPy, NumPy, matplotlib, Libtiff, scikit-learn (sklearn) |
Software |
… License/Openness Free and open source Description Nuclei Segmentation using Deep Learning for individual cell … has topic Machine learning has biological terms nuclei nucleus Additional keywords deep learning Entry … - 19:51 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation with DeepCell Reference Publication Link … |
| Nuclei Tracking (ImageJ) |
5 |
|
3D, time-series |
ImageJ |
Software |
… source has function Object tracking has biological terms nuclei nucleus Entry Curator czhang Post date 02/26/2019 - … processing Download Page Neubias BIAFLOWS workflow of nuclei tracking with ImageJ has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION … lascholz … Bäcker, Volker … 4023 … … |
| NeuriteTracer |
5 |
|
2D |
ImageJ |
Software |
… analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" … topic Fluorescence microscopy has biological terms neuron nuclei Post date 01/28/2018 - 12:18 Last modified 04/27/2023 … |
| StarDist - ImageJ |
5 |
|
2D, 3D |
ImageJ |
Software |
… This is the ImageJ/Fiji plugin for StarDist , a cell/nuclei detection method for microscopy images with … shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained … microscopy Machine learning has biological terms nuclei Entry Curator czhang Post date 03/03/2020 - 16:07 Last … |
| NuclearQuant |
5 |
|
2D |
QuantCenter |
Software |
… is a QuantCenter module. It is designed for cell nuclei detection and quantification of IHC stained samples. … morphological features besides stain intensity. The cell nuclei classification and the final score are calculated by … detection has topic Digital histology has biological terms nuclei tissue Additional keywords whole-slide analysis Entry … |
| Nuclei Segmentation (U-Net) |
5 |
|
2D |
scikit-image, NumPy |
Software |
… has topic Machine learning has biological terms nuclei nucleus Additional keywords deep learning Entry … - 19:48 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation with U-Net Reference Publication Link … in Fluorescence… has comparison Neubias BIAFLOWS Nuclei Segmentation Project … lascholz … 4372 … Paavolainen, … |
| FISH signals detection |
4 |
|
2D |
Fiji |
Software |
… The macro segments and classifies human spermatozoids nuclei (DAPI) based on the number of FISH signals (spots) … as well as the position (point selections) of the detected nuclei falling in these classes. The input image should be an … … The macro segments and classifies human spermatozoids nuclei (DAPI) based on the number of FISH signals (spots) … |
| Nuclei Segmentation (Stardist) |
4 |
|
2D |
|
Software |
… has topic Machine learning has biological terms nuclei nucleus Additional keywords deep learning Entry … BIAFLOWS Benchmarking workflow has comparison BIAFLOWS Nuclei Segmentation project … czhang … 4372 … BIAFLOWS team … … with tensorflow-gpu and/or nvidia-docker images. … Nuclei Segmentation (Stardist) … |
| 2D spots counting using KNIME |
4 |
|
2D |
KNIME Image Processing and Analysis |
Software |
… KNIME workflow solutions are similar: first one detects nuclei and spots inside the nuclei without taking care of surrounding regions, i.e. … KNIME workflow solutions are similar: first one detects nuclei and spots inside the nuclei without taking care of … |
| Imaris |
4 |
|
|
Imaris |
Software |
… and tracking of biological objects such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for … new spots in 3D space. ImarisCell is a tool to detect nuclei, cell boundaries and vesicles and track these through … and tracking of biological objects such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for … |
| u-track |
3.727 |
|
2D, 3D, time-series |
Matlab Image Processing Toolbox, Bio-Formats |
Software |
… tracking (previously distributed as plusTipTracker) and nuclei tracking A third optional processing step has been … 2012 for tracking fluorescently-labeled cell nuclei. has function Affine registration Cell tracking … tracking (previously distributed as plusTipTracker) and nuclei tracking A third optional processing step has been … |
| IdentifyTertiaryObjects |
3 |
|
2D |
CellProfiler |
Software |
… For example allows to segment the cytoplasm by subtracting nuclei from cells. has function Object feature extraction … topic Bioimage informatics has biological terms cytoplasm nuclei Entry Curator czhang Post date 10/11/2013 - 15:08 Last … For example allows to segment the cytoplasm by subtracting nuclei from cells. … IdentifyTertiaryObjects … |
| Bayesian Tracker (btrack) |
3 |
|
2D, time-series |
Python |
Software |
… CNN to allow accurate instance segmentation of the cell nuclei. To track the cells over time and through cell … microscopy Machine learning has biological terms nuclei Additional keywords Deep learning in microscopy Entry … CNN to allow accurate instance segmentation of the cell nuclei. To track the cells over time and through cell … |
| Object Tracking (Octave) |
3 |
|
2D, time-series |
GNU Octave |
Software |
… License/Openness Free and open source Description Nuclei tracking in 2D time-lapse with Octave tracker (adapted … informatics Live sample imaging has biological terms nuclei nucleus Entry Curator lascholz Post date 01/23/2020 - … for large and com… has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION … lascholz … Tosí, Sébastien … 4023 … |
| Find cells using nuclear and membrane fluorescence |
3 |
|
|
|
Software |
… source Description This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and … biological terms nucleus cell membrane Additional keywords nuclei segmentation membrane staining Entry Curator czhang … … Active contours … This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and … |
| Nuclei Tracking (TrackMate) |
3 |
|
2D, time-series |
TrackMate, pyimagej |
Software |
… for single-particle tracking DOI link BIAFLOWS-PROBLEM: NUCLEI-TRACKING-NODIVISION … lascholz … Paavolainen, Lassi … … … Track non-dividing particles in 2D time-lapse image. … Nuclei Tracking (TrackMate) … |
| TANGO Tools for Analysis of Nuclear Genome Organization |
2.969 |
|
3D |
|
Software |
… - Prefiltering - Segmentation - Postfiltering - Isolated nuclei could individually be inspected, deleted from list and … Fluorescence microscopy Statistics has biological terms nuclei Entry Curator czhang Post date 02/18/2015 - 14:10 Last … - Prefiltering - Segmentation - Postfiltering - Isolated nuclei could individually be inspected, deleted from list and … |
| ImmunoRatio |
2 |
|
2D |
ImageJ, Colour Deconvolution |
Software |
… of the total nuclear area , not the percentage of detected nuclei (the latter being the more common method of assessing … of the total nuclear area , not the percentage of detected nuclei (the latter being the more common method of assessing … |
| IdentifyPrimaryObjects |
2 |
|
2D |
CellProfiler, Spot Detector (Icy), Graylevel Watershed for ImageJ |
Software |
… Free and open source Description Identify objects (as nuclei) within an image without needing the assistance of … detection … Fluorescence microscopy … Identify objects (as nuclei) within an image without needing the assistance of … |
| IdentifySecondaryObjects |
2 |
|
2D |
CellProfiler |
Software |
… cells) using objects identified by another module (e.g., nuclei) as a starting point. has function Image segmentation … cells) using objects identified by another module (e.g., nuclei) as a starting point. … IdentifySecondaryObjects … |
| Measure distance of organelles from nucleus in 3D |
2 |
|
3D |
Imaris, MATLAB |
Software |
… detection: Imaris Add a new SURFACE object, name it "nuclei" Follow the object detection wizard to segment nucleus … detection: Imaris Add a new SURFACE object, name it "nuclei" Follow the object detection wizard to segment nucleus … |
| CellProfiler Examples - Speckle Counting |
2 |
|
2D |
CellProfiler |
Software |
… to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a … to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a … |
| Columbus Image Data Storage and Analysis System |
2 |
|
|
|
Software |
… workflows can be developed by combining modules like "find nuclei", "find cytoplasm", "find spots" for object detection. … workflows can be developed by combining modules like "find nuclei", "find cytoplasm", "find spots" for object detection. … |
| SuperDSM |
2 |
|
2D |
Python |
Software |
… on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. has … on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. … … |
| Spot Detector (Icy) |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… noisy images 2D/3D. - Depending on objective, spots can be nuclei, nucleus or cell - Versatile input: sequence or batch … noisy images 2D/3D. - Depending on objective, spots can be nuclei, nucleus or cell - Versatile input: sequence or batch … |
| NucleusJ |
2 |
|
2D, 3D |
Fiji, MorphoLibJ |
Software |
… measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning … measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning … |
| 3D cell tracking using Gaussian Mixture Model (TGMM) |
2 |
|
|
|
Software |
… large 3D volume (typically lightsheet). It detects cell nuclei by fitting gaussians on their fluorescent intensity. … large 3D volume (typically lightsheet). It detects cell nuclei by fitting gaussians on their fluorescent intensity. … |
| Nessys |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to … written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to … |
| Aivia - Aivia Cloud - Aivia Web |
2 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… system cancer neuron developmental biology mitosis synapse nuclei cell volume cell motility cell membrane cell area … computing Image denoising Image restoration label free nuclei prediction web deployment electron microscopy Entry … |
| Object Tracking (ImageJ) |
2 |
|
2D, time-series |
ImageJ |
Software |
… has topic Live sample imaging has biological terms nuclei Entry Curator lascholz Post date 01/23/2020 - 16:10 … Tracking with ImageJ has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION … lascholz … Tosí, Sébastien … 4023 … |
| Analyze Spheroid Cell Invasion In 3D Matrix |
2 |
|
3D |
MorphoLibJ |
Software |
… assay. It can also count and measure the area of the nuclei within the spheroïd. has function Cell segmentation … assay. It can also count and measure the area of the nuclei within the spheroïd. … Analyze Spheroid Cell Invasion … |
| Region Competition |
1 |
|
|
Fiji, MosaicSuite |
Software |
… topic Imaging Fluorescence microscopy has biological terms nuclei zebrafish endosomes cells Entry Curator lplantard Post … |
| ilastik - Automatic Tracking |
1 |
|
2D, 3D, time-series |
ilastik |
Software |
… informatics Supervised learning has biological terms nuclei Entry Curator Moritz Post date 10/15/2013 - 12:45 Last … |
| EBImage |
1 |
|
2D |
Bioconductor |
Software |
… informatics High content screening has biological terms nuclei Entry Curator czhang Post date 09/13/2017 - 09:41 Last … |
| QuantCenter |
1 |
|
2D, multi-channel |
|
Software |
… histology Fixed sample imaging has biological terms tissue nuclei Additional keywords whole-slide analysis Entry Curator … |
| SpotDistance |
1 |
|
3D |
ImageJ |
Software |
… informatics Fluorescence microscopy has biological terms nuclei Entry Curator migration Post date 10/11/2013 - 15:08 … |
| Automatic 2D/3D Tracking using ilastik |
1 |
|
2D, 3D, time-series |
ilastik |
Software |
… Bioimage informatics Machine learning has biological terms nuclei Entry Curator czhang Post date 12/08/2014 - 17:18 Last … |
| Particle Tracking (ImageJ) |
1 |
|
2D, time-series |
ImageJ, FeatureJ Laplacian |
Software |
… Tracking with ImageJ has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-NODIVISION … czhang … Tosí, Sébastien … 4141 … |
| Object Tracking (MU-Lux-CZ) |
1 |
|
2D, time-series |
OpenCV, scikit-image, Tensorflow, Keras |
Software |
… Deep Learning and… has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION … lascholz … Lux, Filip … Matula, … |
| BioImage Model Zoo |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… bacteria Arabidopsis ovules Arabidopsis thaliana neuron nuclei plant cell membrane stem cells vesicles epithelia … |
| ELEPHANT |
1 |
|
2D, 3D, time-series |
|
Software |
… microscopy Machine learning has biological terms nuclei C.elegans embryo development drosophila embryo … |
| ZeroCostDL4Mic |
1 |
|
2D, 3D |
|
Software |
… field microscopy Machine learning has biological terms nuclei neuron Actin tubulin Hela cells Additional keywords … |
| WormGUIDES Atlas |
0.803 |
|
3D, multi-channel, time-series |
|
Software |
… informatics has biological terms c. elegans embryo nuclei Additional keywords cell lineage Entry Curator czhang … |
