| Nuclei Segmentation (Cellpose) |
26 |
|
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 using pre-trained nuclei segmentation models of … |
| Nuclei Segmentation (CellProfiler) |
25 |
|
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 … for Neubias BIAFLOWS Benchmarking tool. has function Image segmentation has biological terms nucleus nuclei Entry … |
| Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ) |
24 |
|
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 … image is written for each input image. has function Cell segmentation Watershed segmentation Morphological operation … |
| Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ) |
24 |
|
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 … image is written for each input image. has function Image segmentation Watershed segmentation Smoothing Entry Curator … |
| Nuclei Segmentation 2D (ImageJ) |
23 |
|
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 … image is written for each input image. has function Image segmentation Watershed segmentation Entry Curator czhang Post … |
| Nuclei Segmentation (Python) |
20 |
|
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 Watershed segmentation Object detection Smoothing has biological terms … |
| Nuclei Segmentation (ilastik) |
17 |
|
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 post-processing. … has topic Machine learning has biological terms nucleus nuclei Additional keywords probability map Entry Curator … |
| Cell or particle counting and scoring the percentage of stained objects |
16.977 |
|
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 … computed using the CalculateMath Module. has function Cell segmentation Object classification Object counting has topic … |
| Nuclei Segmentation (Mask-RCNN) |
16 |
|
2D |
|
Software |
… Free and open source Description NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport … - 17:10 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation with Mask-RCNN Documentation Link Mask … |
| Nuclei Segmentation (U-Net) |
15 |
|
2D |
scikit-image, NumPy |
Software |
… License/Openness Free and open source Description U-Net segmentation as presented in Reference Publication. The model … 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 … |
| Nessys |
14 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… source License GPLv3 Description Nessys: Nuclear Envelope Segmentation System Nessys is a 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 … |
| Nuclei Segmentation (DeepCell) |
14 |
|
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 analysis … has topic Machine learning has biological terms nuclei nucleus Additional keywords deep learning Entry … |
| StarDist - ImageJ |
14 |
|
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 models to new images. has function Image segmentation Cell segmentation Model-based segmentation has … |
| Nuclei Segmentation 3D (NucleiSegmentation3D-ilastik) |
12 |
|
3D |
ilastik |
Software |
… License/Openness Free and open source Description Execute Nuclei Segmentation in 3D images using pixel classification with … - 13:26 Download Page Neubias BIAFLOWS workflow of Nuclei Segmentation 3D with ilastik Reference Publication … |
| SuperDSM |
10 |
|
2D |
Python |
Software |
… License MIT Description SuperDSM is a globally optimal segmentation method based 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. … … |
| Nuclei Segmentation (Stardist) |
10 |
|
2D |
|
Software |
… and/or nvidia-docker images. has function Cell segmentation 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 … … |
| TANGO Tools for Analysis of Nuclear Genome Organization |
9.969 |
|
3D |
|
Software |
… - Construction of workflow in GUI by choosing filters / segmentation strategy for - 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 … |
| Region Competition |
9 |
|
|
Fiji, MosaicSuite |
Software |
… Automated License/Openness I do not know Description Image segmentation based on the MOSAIC Discrete region competition algorithm. has function Image segmentation Cell segmentation has topic Imaging Fluorescence microscopy has biological terms nuclei zebrafish endosomes cells Entry Curator lplantard Post … |
| Aivia - Aivia Cloud - Aivia Web |
9 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Filament tracing Image feature detection Image segmentation Cell segmentation Pixel classification Neuron … 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 … |
| IdentifySecondaryObjects |
8 |
|
2D |
CellProfiler |
Software |
… cells) using objects identified by another module (e.g., nuclei) as a starting point. has function Image segmentation Cell segmentation Object detection has topic … cells) using objects identified by another module (e.g., nuclei) as a starting point. … IdentifySecondaryObjects … |
| IdentifyPrimaryObjects |
8 |
|
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 another cellular feature (as cell). has function Image segmentation Cell segmentation Object detection has topic … detection … Fluorescence microscopy … Identify objects (as nuclei) within an image without needing the assistance of … |
| NuclearQuant |
8 |
|
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 … score and the proportion score. has function Cell segmentation Object classification Object detection has topic … |
| Bayesian Tracker (btrack) |
8 |
|
2D, time-series |
Python |
Software |
… with a classification 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 … |
| Spot Detector (Icy) |
8 |
|
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 … - Displays tags has function Spot detection Image segmentation Cell segmentation has topic Electron microscopy … noisy images 2D/3D. - Depending on objective, spots can be nuclei, nucleus or cell - Versatile input: sequence or batch … |
| Measure distance of organelles from nucleus in 3D |
7.981 |
|
3D |
Imaris, MATLAB |
Software |
… detection: Imaris Add a new SURFACE object, name it "nuclei" Follow the object detection wizard to segment nucleus … approach to avoid this error would incorporate a cell segmentation step to assign certain organelle objects to … detection: Imaris Add a new SURFACE object, name it "nuclei" Follow the object detection wizard to segment nucleus … |
| NucleusJ |
7 |
|
2D, 3D |
Fiji, MorphoLibJ |
Software |
… measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning … the objects within the nuclear volume. has function Image segmentation has topic Bioimage informatics has biological … measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning … |
| Find cells using nuclear and membrane fluorescence |
7 |
|
|
|
Software |
… source Description This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and … channel (membrane-labeling). has function Cell segmentation Active contours has biological terms nucleus cell membrane Additional keywords nuclei segmentation membrane staining Entry Curator czhang … |
| Automatic 2D/3D Tracking using ilastik |
6 |
|
2D, 3D, time-series |
ilastik |
Software |
… for roundish objects or spots. Tracking is done through segmentation, which can be obtained from ilastik pixel … as daughter cells) inherit this ID. has function Image segmentation Object tracking has topic Bioimage informatics Machine learning has biological terms nuclei Entry Curator czhang Post date 12/08/2014 - 17:18 Last … |
| FISH signals detection |
6 |
|
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) … |
| CellProfiler Examples - Speckle Counting |
6 |
|
2D |
CellProfiler |
Software |
… to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a … in the download package. has function Spot detection Image segmentation has topic Bioimage informatics has biological … to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a … |
| EBImage |
6 |
|
2D |
Bioconductor |
Software |
… report-writing system has function Image analysis Image segmentation Image processing Geometrical transformation … informatics High content screening has biological terms nuclei Entry Curator czhang Post date 09/13/2017 - 09:41 Last … … HCS … basic_html … czhang … Image analysis … Image segmentation … Image processing … Geometrical transformation … |
| Nuclei Tracking (ImageJ) |
6 |
|
3D, time-series |
ImageJ |
Software |
… source has function Object tracking has biological terms nuclei nucleus Entry Curator czhang Post date 02/26/2019 - … 2: Threshold smoothed image Thresholder (ImageJ) Image segmentation Step 3: Run Watershed on binary mask Watershed … processing Download Page Neubias BIAFLOWS workflow of nuclei tracking with ImageJ has comparison BIAFLOWS-PROBLEM: … |
| Imaris |
6 |
|
|
Imaris |
Software |
… Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy … 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 … |
| IdentifyTertiaryObjects |
5 |
|
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 … |
| Analyze Spheroid Cell Invasion In 3D Matrix |
5 |
|
3D |
MorphoLibJ |
Software |
… assay. It can also count and measure the area of the nuclei within the spheroïd. has function Cell segmentation Object counting has topic Live sample imaging … assay. It can also count and measure the area of the nuclei within the spheroïd. … Analyze Spheroid Cell Invasion … |
| QuantCenter |
4 |
|
2D, multi-channel |
|
Software |
… analysis. has function Analysis Image classification Cell segmentation Object classification Object detection Pattern … histology Fixed sample imaging has biological terms tissue nuclei Additional keywords whole-slide analysis Entry Curator … … czhang … Analysis … Image classification … Cell segmentation … Object classification … Object detection … … |
| ZeroCostDL4Mic |
4 |
|
2D, 3D |
|
Software |
… to use deep-learning for microscopy. has function Image segmentation Object detection Image denoising Image … field microscopy Machine learning has biological terms nuclei neuron Actin tubulin Hela cells Additional keywords … … Artificial intelligence … basic_html … czhang … Image segmentation … Object detection … Image denoising … Image … |
| BioImage Model Zoo |
4 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… Learning models. has function Image classification Cell segmentation Image denoising has topic Digital histology … bacteria Arabidopsis ovules Arabidopsis thaliana neuron nuclei plant cell membrane stem cells vesicles epithelia … … basic_html … czhang … Image classification … Cell segmentation … Image denoising … Digital histology … Electron … |
| Object Tracking (MU-Lux-CZ) |
2 |
|
2D, time-series |
OpenCV, scikit-image, Tensorflow, Keras |
Software |
… Challenge Page Reference Publication Link DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and… has comparison BIAFLOWS-PROBLEM: NUCLEI-TRACKING-DIVISION … lascholz … Lux, Filip … Matula, … |
