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:
Relevance requires Content type Excerpt
4 … neuron … neuron …
3
4 … dragonfly neuron … dragonfly neuron …
4
2 … structure reconstruction Curvilinear structure detection neuron image analysis neuron reconstruction … Filament tracing …
4 … fruit fly neuron … fruit fly neuron …
4
4 … neuron tracing … neuron tracing …
4 … neuron cell morphology … neuron cell morphology …
Content type: Software
Relevance Supported Image Dimension requires Content type Excerpt
Aivia - Aivia Cloud - Aivia Web 4 2D, 3D, multi-channel, time-series Software … Image segmentation Cell segmentation Pixel classification Neuron image analysis Object classification Object counting … Machine learning has biological terms immune system cancer neuron developmental biology mitosis synapse nuclei cell … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Image feature …
Analyze Complex Roots Tool 2 Concentric circles on the mask of a root, created by the Analyze Complex Roots Tool 2D Fiji Software
AnaMorf 2 AnaMorph 2D, multi-channel, time-series ImageJ Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … basic_html … vcaldas … Filament …
Angiogenesis / Sprout Analyzer (ImageJ) 3 graphical abstract 2D, multi-channel ImageJ Software … cell/pericyte ratio. has function Filament tracing Neuron image analysis has topic Bioimage informatics … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Bioimage analysis … basic_html … …
APP (All-path pruning) 11.634 APP_Vaa3D_example_results 2D, 3D Vaa3D Software … the all-path pruning (APP), to trace the 3D structure of a neuron. To avoid potential mis-tracing of some parts of a neuron, an APP first produces an initial over-reconstruction, … has function Filament tracing Image thresholding Neuron image analysis has topic Confocal microscopy has …
APP2 9.779 APP2_Vaa3D_example_Result 2D, 3D Vaa3D Software … of Vaa3D. APP2 prunes an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical … or user-defined parameters. has function Filament tracing Neuron image analysis Distance transform has topic Confocal microscopy has biological terms dragonfly neuron drosophila Additional keywords Gray-weighted distance …
BioCat 1 need a thumbnail 2D, 3D Software
BioImage Model Zoo 1 need a thumbnail 2D, 3D, multi-channel, time-series Software … bacteria Arabidopsis ovules Arabidopsis thaliana neuron nuclei plant cell membrane stem cells vesicles …
CATMAID 0.903 CATMAID 2D, 3D Software … Light-sheet microscopy has biological terms synapse neuron drosophila Entry Curator czhang Post date 11/07/2013 - …
CellProfiler 1 2D, 3D, multi-channel, time-series Software
CEM 3 Myelin 2D, 3D, multi-channel ImageJ Software … detailed user manual and the download link . has function Neuron image analysis Dilation Pixel-based colocalisation … analysis … Co-localisation analysis … HCS … basic_html … Neuron image analysis … Dilation … Pixel-based colocalisation …
ClearMap 2.997 ClearMap SCreenshot 3D, multi-channel OpenCV, scikit-image Software … Image analysis Filament tracing Cell segmentation Neuron image analysis Data handling Image stitching … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Plotting … LSFM … Digitally scanned …
FibrilTool 2 2D ImageJ Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Manual segmentation … Slide scanner … …
Filament Tracing (ImageJ) 2 need a thumbnail 3D ImageJ Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Gaussian filtering … Gaussian …
Filament Tracing LocThresh (ImageJ) 2 need a thumbnail 3D ImageJ Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Medial axis … Bioimage analysis … …
Filament Tracing Tubeness (ImageJ) 2 need a thumbnail 3D ImageJ, Tubeness Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Edge enhancement … Steerable fliter … …
Filopodyan 2 2D, time-series ImageJ, Fiji Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … basic_html … Perrine … …
hIPNAT 7 need a thumbnail 2D, multi-channel, time-series ImageJ Software … Neuroanatomy update site . has function Filament tracing Neuron image analysis Object feature extraction has topic … terms neurons Additional keywords tree-like structure neuron tracing filament network Post date 09/12/2017 - 10:12 … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Feature …
HyphaTracker 2 hyphatracker 2D, time-series ImageJ Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … Image pre-processing … …
ilastik 1.862 2D, 3D, multi-channel, time-series VIGRA Software
ilastik - Carving 3 need a thumbnail 2D, 3D ilastik Software … Bioimage informatics Machine learning has biological terms neuron blood vessels plant tubular structure Entry Curator …
ImageJ Analyze Skeleton 2.969 2D, 3D ImageJ, Analyze 12.0 Software … has biological terms gland filament blood vessels neuron mitochondria cytoskeleton Entry Curator vcaldas Post … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Pixel labeling … Voxel classification …
Imaris 4 null Imaris Software
ImarisFilamentTracer 2 need a thumbnail Imaris, Sholl Analysis (ImageJ) Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Bioimage analysis … alban.gaignard … …
JFilament 3 JFilament_ImageJ_pulgin_Window 2D, 3D, time-series ImageJ Software …   has function Filament tracing Active contours Neuron image analysis Additional keywords Open curve … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Active contour model … Active contour …
Junction Mapper 2 junction mapper 2D, multi-channel Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Feature detection … Image labeling … …
KNOSSOS - 3D image visualization and annotation tool 2 Annotation in Knossos 3D Software
Measure cell volume over time 4 3D, time-series ImageJ, Imaris Software
MeasureNeurons (CellProfiler) 6 need a thumbnail 2D CellProfiler Software … are available in the discussion. Measure Neurons - Total Neuron Length Measurement has function Neuron image analysis Object feature extraction has topic Bioimage informatics has biological terms neuron Entry Curator migration Post date 10/11/2013 - 15:08 …
Microtubule Length Analysis 2 need a thumbnail 2D, 3D Fiji, Tubeness Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Medial axis … Bioimage analysis … …
Microtubules Tool (3D) 3 3D microtubules 3D, multi-channel ImageJ, Fiji, Skeletonize3D, 3D Objects Counter Software … has biological terms microtubules cell migration neuron cytoskeleton Additional keywords morphometry Entry … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Thresholding … Clustering-based image …
MicrotubuleTracker in FIJI 2 Track Filament shaped objects and analyze tracks using Ransac fits. 2D, 3D, time-series Fiji Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … basic_html … kapoorlab … …
MiToBo 1 2D, 3D Fiji Software … has biological terms cell migration cytoskeleton neuron neurites filament Entry Curator czhang Post date …
MosaicSuite 2 2D, 3D, time-series Fiji, ImageJ 2.x Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Seed point detection … Flat field …
MOST-Raytracer 2 need a thumbnail 3D Vaa3D Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Image restoration … basic_html … …
NBLAST 7 3D NeuroAnatomy Toolbox Software … source Description This R package implements the NBLAST neuron similarity algorithm described in a preprint available … … Statistics … This R package implements the NBLAST neuron similarity algorithm described in a preprint available …
nctuTW 18.641 nctuTW_results_example 3D Vaa3D Software … methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal … in the image stack do not reflect the true shape of the neuron. This is the main reason we chose not to work directly … of voxels that is a superset of the 3D centerlines of the neuron. The shortest path graph algorithm then computes the …
NET - Network Extraction Tool 2 need a thumbnail 2D Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Thresholding … Clustering-based image …
Neural Circuit Tracer 5.993 Example of output from Neural Circuit Tracer 3D Matlab compiler runtime Software … images. NCTracer has more than one workflow available for neuron tracing.  "The Neural Circuit Tracer is open source … the Neural Circuit Tracer."  has function Filament tracing Neuron image analysis Image enhancement has topic Confocal … axons neuromuscular axons olfactory axons drosophila neuron Additional keywords Active contours Filament …
NeuriteTracer 12 2D ImageJ Software … on the related publication) has function Filament tracing Neuron image analysis Image processing Smoothing … has topic Fluorescence microscopy has biological terms neuron nuclei Post date 01/28/2018 - 12:18 Last modified … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Image …
NeuroAnatomy Toolbox 2 3D, multi-channel Software
Neuroglancer 1 Neuroglancer Software … microscopy Light-sheet microscopy has biological terms neuron skeleton Entry Curator Perrine Post date 08/07/2019 - …
NeuroGPS-Tree 3 need a thumbnail 3D Vaa3D Software
Neurolucida 9 Neurolucida example 2D, 3D, multi-channel, time-series Software … and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform … 10.3389/fnins.2012.00049 has function Cell segmentation Neuron image analysis Object feature extraction has topic … has biological terms neurons Additional keywords neuron cell morphology morphometry Entry Curator devrim Post …
Neuron Tracing 3D (ImageJ) 8 need a thumbnail 3D ImageJ Software … Free and open source has function Filament tracing Neuron image analysis Feature enhancement has biological terms neuron Entry Curator lascholz Post date 02/26/2019 - 15:39 … Skeleton Download Page Neubias BIAFLOWS workflow of Neuron Tracing 3D with ImageJ has comparison BIAFLOWS Neuron …
Neuron Tracing 3D (Rivuletpy) 9 need a thumbnail 3D Software … workflow for BIAFLOWS. has function Filament tracing Neuron image analysis has topic Machine learning has biological terms neuron filament Entry Curator czhang Post date 01/23/2020 - … - 20:30 Download Page Neubias BIAFLOWS workflow of Neuron Tracking with Rivuletpy (Rivulet 2) Reference …
Neuron Tracing Vaa3D (App2) 9 need a thumbnail 3D Vaa3D, APP2 Software … workflow for BIAFLOWS. has function Filament tracing Neuron image analysis has topic Bioimage informatics has biological terms neuron Additional keywords Graph-based tracing Entry Curator … - 19:43 Download Page Neubias BIAFLOWS workflow of Neuron Tracking with Vaa3d APP2 Reference Publication Link …
Neuron Tracing Vaa3D (BJUT FM Spanning Tree) 8 need a thumbnail 3D Vaa3D Software … workflow for BIAFLOWS has function Filament tracing Neuron image analysis has topic Bioimage informatics has biological terms filament neuron Additional keywords Fast marching method Level set … - 18:17 Download Page Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d BJUT Fast Marching Spann… has …
Neuron Tracing Vaa3D (MOST) 8 need a thumbnail 3D Vaa3D, MOST-Raytracer Software … License/Openness Free and open source Description 3D Neuron Tracing with a Dockerized version of Vaa3D MOST Raytracer. has function Filament tracing Neuron image analysis Entry Curator lascholz Post date … - 18:27 Download Page Neubias BIAFLOWS workflow of Neuron Tracing with Vaa3d MOST Reference Publication Link 3D …
Neuron Tracing Vaa3D (MST) 9 need a thumbnail 3D Vaa3D Software … License/Openness Free and open source Description 3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST). has function Filament tracing Neuron image analysis has topic Bioimage informatics has biological terms neuron filament Entry Curator czhang Post date 01/23/2020 - …
NeuronJ 8 2D ImageJ Software … has topic Bioimage informatics has biological terms neuron Additional keywords quantification 8 bit Entry Curator … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Bioimage analysis … migration … …
NeuronMetrics 8 need a thumbnail 2D Software … from image artifacts.   has function Filament tracing Neuron image analysis Shape features has topic Imaging has … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Area … basic_html … Filament tracing …
NeuronStudio 13.802 NeuronStudio_standaloneapp_window_overview 2D, 3D Software … when using it. You may not decompile, disassem Description Neuron studio is a software package to reconstruct neurons … (Fully or semi-automated). has function Filament tracing Neuron image analysis Skeletonisation has topic Confocal microscopy has biological terms filament neuron skeleton Additional keywords rayburst sampling Entry …
NeurphologyJ 4 ImageJ Software … neurite attachment points Additional keywords morphometry neuron cell morphology branching Entry Curator kota Post date …
neuTube (or NeuTu) 10 Neutube_standaloneapp_window_overview 2D, 3D 3D Viewer Software … attributed. Description neuTube is a collection of neuron reconstruction tools from fluorescence microscope … with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can … used as a plugin in Vaa3D.   has function Filament tracing Neuron image analysis Editing has topic Bioimage informatics …
ORION 15.946 ORION_example_result 3D Software … A project to develop tools that explore single neuron function via sophisticated image analysis. ORION … of an acute experiment. has function Filament tracing Neuron image analysis Image deconvolution Image enhancement … Github repository page Reference Publication Link Live Neuron Morphology Automatically Reconstructed From …
Paintera 5.889 Paintera screenshot 3D JavaFX, Maven Software … in segmentation/reconstruction with a primary focus on neuron reconstruction from  electron micrographs  in  … of the UI framework  JavaFX has function Filament tracing Neuron image analysis Image reconstruction Image … microscopy In-silico reconstruction has biological terms neuron Additional keywords connectomics Entry Curator …
Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment 1 2D, time-series ImageJ, Excel Software
Phindr3D 2.819 3D, multi-channel MATLAB Software … analysis Image classification Image feature detection Neuron image analysis Classification Clustering Image … … Image classification … Image feature detection … Neuron image analysis … Classification … Clustering … Image …
Reconstruct 3 Reconstruct_standaloneapp_example_Results 3D Software … algorithm called wildfire." has function Filament tracing Neuron image analysis has topic Scanning electron microscopy … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … basic_html … lascholz … Filament …
Rivulet 10.692 Traceplot_Rivulet 3D MATLAB Software … Apache 2.0 Description "we propose a novel automatic 3D neuron reconstruction algorithm, named Rivulet, which is … Wiki website ( https://github.com/RivuletStudio/Rivulet-Neuron-Tracing-Toolbox/wiki )  has function Filament tracing Neuron image analysis has topic Confocal microscopy Machine …
Rivulet 2 (Rivuletpy) 5 3D SciPy, NumPy, Python, Libtiff, simpleITK, cython Software … License has function Filament tracing Image thresholding Neuron image analysis Distance transform has biological terms neuron olfactory projection fibres Entry Curator lascholz … Github repository Reference Publication Link Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence …
Sholl Analysis (ImageJ) 9.997 sholl analysis 2D, 3D ImageJ Software … has biological terms neuronal arbors neurite arbor neuron Entry Curator migration Post date 10/11/2013 - 15:08 … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Image feature extraction … basic_html …
Simple Neurite Tracer 5.993 2D, 3D Fiji Software … has topic Bioimage informatics has biological terms neuron neurites filament microtubules cytoskeleton Additional … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Plotting … Bioimage analysis … …
Simple Tracing DF-Tracing 8.92 Simple Tracing - DT-fields 3D Vaa3D Software … extracted foreground neurite signal and reconstructs the neuron morphology automatically. Two distance-transform based … can“push” a “rolling ball” quickly along the skeleton of a neuron, reconstructing the 3D cell morphology. has function … tracing Image segmentation Adaptative thresholding Neuron image analysis Image enhancement Distance transform …
SOAX 2 snapshot microtubules soax 2D, 3D Active Contours Software … reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Active contour model … Active contour …
Spine classification based on kernel density estimation 1 2D MATLAB, Matlab Image Processing Toolbox Software … two-photon images of dendritic spines has function Neuron image analysis Classification has biological terms … … 4426 … M U Ghani … 4026 … 4087 … basic_html … devrim … Neuron image analysis … Classification … We propose to use a …
SR-Tesseler 2 Density map of a neuron extracted from the Voronoï diagram 2D Software
Strahler Analysis 1 2D, 3D ImageJ, Skeletonize3D, ImageJ Analyze Skeleton Software … biological terms neuroanatomy cytoskeleton blood vessels neuron filament Additional keywords binary images 8 bit Entry …
SynActJ 1 SynActJ workflow 2D, time-series Fiji Software … and plotted using an R Shiny workflow.  has function Neuron image analysis has topic Live sample imaging has … Christopher … 4026 … 4043 … basic_html … schmiedc … Neuron image analysis … Live sample imaging … SynActJ …
SynPAnal 1 need a thumbnail 2D Software … Confocal fluorescence microscopy has biological terms neuron synapse Entry Curator flevet Post date 10/11/2016 - …
TReMAP 10.664 Example_TReMAP_Result 3D Vaa3D Software … are reduced dramatically."  Suitable for high throughput neuron image analysis (image sizes >10GB). This plugin can be … has function Filament tracing Image thresholding Neuron image analysis has topic Confocal microscopy has biological terms neuron dragonfly neuron Additional keywords Minimum spanning …
Tubeness 2 2D, 3D ImageJ Software
Vaa3D 2.864 Vaa3D_logo 2D, 3D, multi-channel, time-series Vaa3D, ITK, ICY Annotation, 3D Viewer Software … powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative … Bioimage informatics Statistics has biological terms brain neuron Entry Curator kota Post date 09/12/2017 - 02:02 Last … powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative …
VMTK: Vascular Modeling Toolkit 1 3D ITK Software … interact with each other   has function Image segmentation Neuron image analysis Visualisation Volume rendering has … … basic_html … julien colombelli … Image segmentation … Neuron image analysis … Visualisation … Volume rendering … …
webKnossos: 3D image annotation, visualization and sharing 1 2D, 3D, multi-channel Software …   has function Image segmentation Interactive segmentation Neuron image analysis Image annotation Data handling … … Image segmentation … Interactive segmentation … Neuron image analysis … Image annotation … Data handling … …
WIS-NeuroMath 3 MATLAB Software
ZeroCostDL4Mic 1 need a thumbnail 2D, 3D Software … microscopy Machine learning has biological terms nuclei neuron Actin tubulin Hela cells Additional keywords Deep …
Content type: Dataset
Relevance requires Content type Excerpt
CREMI challenge 9 cremi samples A and B Dataset … is performed not only by evaluating the quality of neuron segmentations, but also by assessing the accuracy of … adult Drosophila melanogaster brain tissue, comprising neuron segmentation ground truth and annotations for synaptic … in electron microscopy volumes. Image has Ground truth Neuron segmentation Synaptic cleft segmentation Synaptic …
Diadem challenge 8 Diadem challenge Dataset … collections from different animal species, brain regions, neuron types, and visualization methods. Cerebellar climbing … challenge data sets has imaging details Imaging varies by neuron type and species, includes: Transmitted light … 2-photon laser scanning has biological terms neurite arbor neuron fiber … johnbogovic … basic_html … Comprises six data …
SNEMI3D: 3D Segmentation of neurites in EM images 0.95 SNEMI3D Dataset … has imaging details Volume EM has biological terms neuron neurites … Perrine … basic_html … In this challenge, a …
two-photon images of dendritic spines 3 MIP example Dataset
Content type: Basic page
Relevance requires Content type Excerpt
Documentation: Roles, Entry standard and how to curate (read first) 3.348 Basic page … of the software, e.g. "The neuTube is a collection of neuron reconstruction tools from fluorescence microscope … with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can … compilation." example 2: "All-path-pruning 2.0 (APP2) is neuron tracing (fully automated) component of Vaa3D. APP2 …