Search Results

The following table gives you a limited number of fields, you will get further info by clicking on the name of the tool. They are sorted by relevance, which is a simple score counting the number of time your search term appears in the tool description. If the search term appears in title or in tags, it will count twice.
Content type: Software
Relevance Supported Image Dimension requires Content type Excerpt
nctuTW 18.641 nctuTW_results_example 3D Vaa3D Software
ORION 15.946 ORION_example_result 3D Software
NeuronStudio 15.802 NeuronStudio_standaloneapp_window_overview 2D, 3D Software
Neurolucida 15 Neurolucida example 2D, 3D, multi-channel, time-series Software
NeuriteTracer 12 2D ImageJ Software
APP (All-path pruning) 11.634 APP_Vaa3D_example_results 2D, 3D Vaa3D Software
neuTube (or NeuTu) 10.91 Neutube_standaloneapp_window_overview 2D, 3D 3D Viewer Software
Rivulet 10.692 Traceplot_Rivulet 3D MATLAB Software
TReMAP 10.664 Example_TReMAP_Result 3D Vaa3D Software
NeuroGPS-Tree 10 need a thumbnail 3D Vaa3D Software
Sholl Analysis (ImageJ) 9.997 sholl analysis 2D, 3D ImageJ Software
APP2 9.779 APP2_Vaa3D_example_Result 2D, 3D Vaa3D Software
Neuron Tracing Vaa3D (App2) 9 need a thumbnail 3D Vaa3D, APP2 Software
Neuron Tracing 3D (Rivuletpy) 9 need a thumbnail 3D Software
Neuron Tracing Vaa3D (MST) 9 need a thumbnail 3D Vaa3D Software
hIPNAT 9 need a thumbnail 2D, multi-channel, time-series ImageJ Software
Simple Tracing DF-Tracing 8.92 Simple Tracing - DT-fields 3D Vaa3D Software
NeuronMetrics 8 need a thumbnail 2D Software
NBLAST 8 3D NeuroAnatomy Toolbox Software
Neuron Tracing 3D (ImageJ) 8 need a thumbnail 3D ImageJ Software
Neuron Tracing Vaa3D (MOST) 8 need a thumbnail 3D Vaa3D, MOST-Raytracer Software
Neuron Tracing Vaa3D (BJUT FM Spanning Tree) 8 need a thumbnail 3D Vaa3D Software
AutoNeuriteJ 8 2D ImageJ Software
NeuronJ 8 2D ImageJ Software
Neural Circuit Tracer 7.899 Example of output from Neural Circuit Tracer 3D Matlab compiler runtime Software
NeuroAnatomy Toolbox 7 3D, multi-channel Software
NeuroMorph 7 3D Blender Software
WIS-NeuroMath 7 MATLAB Software
Neuroconductor 6.889 2D R Project for Statistical Computing Software
Neuroglancer 6 Neuroglancer Software
MeasureNeurons (CellProfiler) 6 need a thumbnail 2D CellProfiler Software
Simple Neurite Tracer 5.969 2D, 3D Fiji Software
Paintera 5.889 Paintera screenshot 3D JavaFX, Maven Software
Rivulet 2 (Rivuletpy) 5 3D SciPy, NumPy, Python, Libtiff, simpleITK, cython Software
Measure cell volume over time 4.953 3D, time-series ImageJ, Imaris Software
Aivia - Aivia Cloud - Aivia Web 4 2D, 3D, multi-channel, time-series Software
NeurphologyJ 4 ImageJ Software
Imaris 4 null Imaris Software
JFilament 3 JFilament_ImageJ_pulgin_Window 2D, 3D, time-series ImageJ Software
Reconstruct 3 Reconstruct_standaloneapp_example_Results 3D Software
CEM 3 Myelin 2D, 3D, multi-channel ImageJ Software
Microtubules Tool (3D) 3 3D microtubules 3D, multi-channel ImageJ, Fiji, Skeletonize3D, 3D Objects Counter Software
SNT 3 Schematic Overview of SNT components and SNT functionality 2D, 3D Fiji Software … Sholl Analysis doi:10.1038/nmeth.3125 Cx3D doi:10.3389/neuro.10.025.2009 Tubular Geodesics doi:10.1109/cvpr.2012.6 …
Angiogenesis / Sprout Analyzer (ImageJ) 3 graphical abstract 2D, multi-channel ImageJ Software
ilastik - Carving 3 need a thumbnail 2D, 3D ilastik Software
ClearMap 2.997 ClearMap SCreenshot 3D, multi-channel OpenCV, scikit-image Software
ImageJ Analyze Skeleton 2.969 2D, 3D ImageJ, Analyze 12.0 Software
Vaa3D 2.864 Vaa3D_logo 2D, 3D, multi-channel, time-series Vaa3D, ITK, ICY Annotation, 3D Viewer Software
Phindr3D 2.819 3D, multi-channel MATLAB Software
MosaicSuite 2 2D, 3D, time-series Fiji, ImageJ 2.x Software
Amira 2 Amira's interface 2D, 3D, multi-channel, time-series Software
AnaMorf 2 AnaMorph 2D, multi-channel, time-series ImageJ Software
NET - Network Extraction Tool 2 need a thumbnail 2D Software
Tubeness 2 2D, 3D ImageJ Software
MOST-Raytracer 2 need a thumbnail 3D Vaa3D Software
MicrotubuleTracker in FIJI 2 Track Filament shaped objects and analyze tracks using Ransac fits. 2D, 3D, time-series Fiji Software
2D brain slice region annotation: SliceMap 2 Example: SliceMaps brain region segmentation 2D Software
HyphaTracker 2 hyphatracker 2D, time-series ImageJ Software
Ctrax - Caltech Multiple Fly Tracker 2 need a thumbnail Software
FluoRender 2 FluoRenderer 3D Software
SR-Tesseler 2 Density map of a neuron extracted from the Voronoï diagram 2D Software
Filament Tracing (ImageJ) 2 need a thumbnail 3D ImageJ Software
KNOSSOS - 3D image visualization and annotation tool 2 Annotation in Knossos 3D Software
Filopodyan 2 2D, time-series ImageJ, Fiji Software
Filament Tracing Tubeness (ImageJ) 2 need a thumbnail 3D ImageJ, Tubeness Software
Filament Tracing LocThresh (ImageJ) 2 need a thumbnail 3D ImageJ Software
Analyze Complex Roots Tool 2 Concentric circles on the mask of a root, created by the Analyze Complex Roots Tool 2D Fiji Software
Junction Mapper 2 junction mapper 2D, multi-channel Software
Trace Ridges 2 2D Software
Microtubule Length Analysis 2 need a thumbnail 2D, 3D Fiji, Tubeness Software
FibrilTool 2 2D ImageJ Software
SOAX 2 snapshot microtubules soax 2D, 3D Active Contours Software
ImarisFilamentTracer 2 need a thumbnail Imaris, Sholl Analysis (ImageJ) Software
Strahler Analysis 2 2D, 3D ImageJ, Skeletonize3D, ImageJ Analyze Skeleton Software
ilastik 1.862 2D, 3D, multi-channel, time-series VIGRA Software
Spine classification based on kernel density estimation 1 2D MATLAB, Matlab Image Processing Toolbox Software
VMTK: Vascular Modeling Toolkit 1 3D ITK Software
elastix 1 elastix logo 2D, 3D, multi-channel Software
BioCat 1 need a thumbnail 2D, 3D Software
MiToBo 1 2D, 3D Fiji Software
SynPAnal 1 need a thumbnail 2D Software
BioImage Model Zoo 1 need a thumbnail 2D, 3D, multi-channel, time-series Software
webKnossos: 3D image annotation, visualization and sharing 1 2D, 3D, multi-channel Software
SynActJ 1 SynActJ workflow 2D, time-series Fiji Software
ZeroCostDL4Mic 1 need a thumbnail 2D, 3D Software
aNMJ-Morph 1 need a thumbnail 2D, multi-channel ImageJ Software
Colocalization Colormap 1 Icon of the Colocalization Colormap Olugin 2D Software
Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment 1 2D, time-series ImageJ, Excel Software
CellProfiler 1 2D, 3D, multi-channel, time-series Software
CATMAID 0.903 CATMAID 2D, 3D Software
Content type: Dataset
Relevance requires Content type Excerpt
Diadem challenge 10 Diadem challenge Dataset
CREMI challenge 9 cremi samples A and B Dataset
two-photon images of dendritic spines 4 MIP example Dataset
SNEMI3D: 3D Segmentation of neurites in EM images 2.95 SNEMI3D Dataset … of each neurite in the image stack by an expert human neuro-anatomist. The  image data  used in the challenge was … of each neurite in the image stack by an expert human neuro-anatomist. The  image data  used in the challenge was …
LIVECell 0.836 LIvecelldatabase Dataset
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Content type: Basic page
Relevance requires Content type Excerpt
Documentation: Roles, Entry standard and how to curate (read first) 3.348 Basic page