Finding and Reusing specific content

In this demo, we show how we can use the BioImaging EDAM ontology to filter specific tools from the Neubias catalog. COMULIS is a scientific community interested in the field of correlative multimodal imaging. Several image processing and analysis tasks are involved such as image registration, segmentation or visualisation.

Segmentation softwares

EBImage High content screening Bioimage informatics Cell segmentation
2D brain slice region annotation: SliceMap Widefield microscopy Image segmentation
2D cell tracking and analysis of morphological dynamics Active contours Cell segmentation
ANTs: Advanced Normalization Tools Bioimage informatics Image segmentation
APP (All-path pruning) Confocal microscopy Image thresholding
Adaptive Thresholding (EBImage) Cell segmentation Adaptative thresholding
Adipocyte quantification ImageJ by Baecker Digital histology Cell segmentation
Adipocyte quantification MATLAB Digital histology Cell segmentation
Adiposoft Digital histology Watershed Cell segmentation Image thresholding
Aivia Machine learning Cell segmentation Image segmentation
Arabidopsis Seedlings Tool Bioimage informatics Image thresholding
Blob segmentation Image segmentation
Blood vessel segmentation and network analysis Image segmentation
Cell or particle counting and scoring the percentage of stained objects Fluorescence microscopy Cell segmentation
Cell segmentation and quantification with CellX Bright field microscopy Phase contrast microscopy Image segmentation
Cell segmentation in phase contrast images Phase contrast microscopy Active contours Cell segmentation
CellProfiler Examples - Speckle Counting Image segmentation
Counting Clumped Cells Cell segmentation
DNA MicroArray Image Processing Case Study Image segmentation
FibrilTool Statistics Microscopy Interactive segmentation
Find cells using nuclear and membrane fluorescence Active contours Cell segmentation
Find, Draw and Measure Wells in a Multi-Well Plate Picture Image segmentation
FlyLimbTracker Fluorescence microscopy Microscopy Interactive segmentation Active contours
FreeD Bioimage informatics Image segmentation
Golgi Segmentation by Active Mask framework Cell segmentation
HyphaTracker Light microscopy Bright field microscopy Image segmentation
ICY Active Cells SDK Active contours Image segmentation
ITK Image thresholding Image segmentation
ImagePy Bioimage informatics Image segmentation
ImmunoMembrane Digital histology Cell segmentation
JFilament Active contours
Leaf Segmentation using Trainable Weka Segmentation plugin Machine learning Image segmentation
LimeSeg Image segmentation
Lymphatic Vessel Density calculation Digital histology Image segmentation
MAARS Machine learning Bright field microscopy Cell segmentation
MATLAB CellDetector Digital histology Machine learning Fluorescence microscopy Phase contrast microscopy Cell segmentation
MATLAB Image Segmentation Tutorial Image segmentation
MIPAV Computerized tomography Bioimage informatics Magnetic resonance imaging Imaging Image thresholding Image segmentation
MOST-Raytracer Tomography Imaging Image segmentation
Mahotas Watershed Image thresholding
McLuigi Electron microscopy Image segmentation
Measure Rosette Area Tool Bioimage informatics Image thresholding
Microscopy Image Browser (MIB) Topic Image segmentation
Microtubule Length Analysis Image segmentation
Microtubules Tool (3D) Bioimage informatics Image thresholding
MorphoLibJ Bioimage informatics Microscopy Watershed Cell segmentation Image segmentation
MorphoLibJ: using morphological reconstructions to isolate objects Image segmentation
NET - Network Extraction Tool Digital histology Image thresholding
Neuroconductor Bioimage informatics Image segmentation
NiftyNet Machine learning Magnetic resonance imaging Imaging Image segmentation
Object Classification using ilastik Image segmentation
OpenCV / Image Processing Watershed Image thresholding
Orbit Digital histology Machine learning Interactive segmentation Cell segmentation
Oufti Fluorescence microscopy Bright field microscopy Cell segmentation
PHANTAST for FIJI Phase contrast microscopy Cell segmentation
Pixel Classification using ilastik Image segmentation
Protein Micro-array Analysis Image segmentation
QCAnet Machine learning Fluorescence microscopy Image segmentation
QuPath Digital histology Interactive segmentation Cell segmentation
Quantitative analysis of focal adhesions Fluorescence microscopy Image thresholding Image segmentation
QuimP Fluorescence microscopy Interactive segmentation Cell segmentation
Rivulet 2 Image thresholding
SLDC (Segment Locate Dispatch Classify) Machine learning Cell segmentation
SOAX Fluorescence microscopy Confocal fluorescence microscopy Active contours
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh Fluorescence microscopy Image segmentation
Segmentation of Clustered Cells in MATLAB Fluorescence microscopy Watershed Cell segmentation
Simple Tracing DF-Tracing Adaptative thresholding Image segmentation
Splitting clustered cells Watershed
Spot Detector Light microscopy Electron microscopy Bright field microscopy Cell segmentation Image segmentation
Squassh Cell segmentation
SuRVoS Serial block-face scanning electron microscopy Electron tomography Electron microscopy Focused ion beam scanning electron microscopy Machine learning Scanning electron microscopy Cryo electron tomography Interactive segmentation Image segmentation
TReMAP Confocal microscopy Image thresholding
Tensorflow Machine learning Image segmentation
Tissue Cell Segmentation Fluorescence microscopy Watershed Image segmentation
Track cell intensity Active contours
Tracking of focal adhesions in 2D time lapse movies Image segmentation
Trainable Weka Segmentation Machine learning Image segmentation
VMTK: Vascular Modeling Toolkit Light-sheet microscopy Magnetic resonance imaging Image segmentation
Voronoi Segmentation (KNIME) Digital histology Image segmentation
WIS-NeuroMath Image segmentation
WIS-PhagoTracker Image segmentation
Wound healing assay: analysis in CellProfiler Topic Image segmentation
Wound healing assay: analysis in ImageJ Image segmentation
ZEN Intellesis Trainable Segmentation Digital histology Fluorescence microscopy Electron microscopy High content screening Machine learning Light microscopy Image segmentation
classification of hemp fibers based on morphological features Microscopy Watershed
cvMatch_Template Electron microscopy Image segmentation
ilastik Digital histology Machine learning In-silico reconstruction Image segmentation
ilastik - Carving Interactive segmentation Image segmentation
slideToolkit Digital histology Image segmentation

Registration softwares

2D brain slice region annotation: SliceMap Widefield microscopy Image registration
ANTs: Advanced Normalization Tools Bioimage informatics Affine registration Rigid registration Image registration Deformable registration
Align slices in stack Image registration
BigDataViewer Light-sheet microscopy Imaging Affine registration Rigid registration Image registration
BigStitcher Affine registration Rigid registration Image registration
Bigwarp Correlative Light and Electron Microscopy Electron microscopy Image registration Deformable registration
CMTK Statistics Bioimage informatics Affine registration Image registration Deformable registration
CellProfiler Align Rigid registration
FMRIB's Linear Image Registration Tool FLIRT Magnetic resonance imaging Image registration
FNIRT Magnetic resonance imaging Image registration Deformable registration
Fiji CMTK GUI Imaging Affine registration Image registration Deformable registration
FreeD Bioimage informatics Object registration Deformable registration
ITK Image registration
Image Stabilizer Image registration
ImageJ Align RGB planes Rigid registration
KNIME align image Image registration
MIPAV Computerized tomography Bioimage informatics Magnetic resonance imaging Imaging Image registration
Manual Frame Drift Registration Image registration
Morpholeaf Bioimage informatics Image registration
Multiview Reconstruction Light-sheet microscopy Affine registration Rigid registration Image registration
Register Virtual Stack Slices Image registration
Spark Stitcher Light-sheet microscopy Light microscopy Image registration
Template Matching and Slice Alignment--- ImageJ Plugins Image registration
TeraStitcher Rigid registration Image registration
eC-CLEM Correlative Light and Electron Microscopy Affine registration Deformable registration
ec-clem autofinder Correlative Light and Electron Microscopy Affine registration Rigid registration Image registration
elastix Affine registration Image registration Deformable registration
performing automatic registration for CLEM Correlative Light and Electron Microscopy Affine registration Rigid registration Image registration
pystackreg Fluorescence microscopy Electron microscopy Affine registration Rigid registration Image registration
simpleElastix Affine registration Rigid registration

Visualisation softwares

Aivia Machine learning Volume rendering Image visualisation
BigDataViewer Light-sheet microscopy Imaging Image visualisation
ClearVolume Light-sheet microscopy Light microscopy Microscopy Volume rendering
Docker ParaViewWeb Bioimage informatics Image visualisation
Drishti Tomography Electron microscopy Electron tomography Volume rendering Image visualisation
FigureJ Data sharing Montage
ICY 3D Rotation Volume rendering
MIPAV Computerized tomography Bioimage informatics Magnetic resonance imaging Imaging Image visualisation
MaMuT Light-sheet microscopy Live sample imaging Overlay Image visualisation
Magic Montage Data sharing Montage
ScientiFig Data sharing Montage
VMTK: Vascular Modeling Toolkit Light-sheet microscopy Magnetic resonance imaging Volume rendering