ZeroCostDL4Mic |
1 |
|
2D, 3D |
|
Software |
… microscopy Machine learning has biological terms nuclei neuron Actin tubulin Hela cells Additional keywords Deep … |
WIS-NeuroMath |
3 |
|
|
MATLAB |
Software |
|
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 … … |
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 … … |
Vaa3D |
2.864 |
|
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 … |
Tubeness |
2 |
|
2D, 3D |
ImageJ |
Software |
|
TReMAP |
10.664 |
|
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 … |
SynPAnal |
1 |
|
2D |
|
Software |
… Confocal fluorescence microscopy has biological terms neuron synapse Entry Curator flevet Post date 10/11/2016 - … |
SynActJ |
1 |
|
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 … |
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 … |
SR-Tesseler |
2 |
|
2D |
|
Software |
|
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 … |
SOAX |
2 |
|
2D, 3D |
Active Contours |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Active contour model … Active contour … |
Simple Tracing DF-Tracing |
8.92 |
|
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 … |
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 … … |
Sholl Analysis (ImageJ) |
9.997 |
|
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 … |
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 … |
Rivulet |
10.692 |
|
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 … |
Reconstruct |
3 |
|
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 … |
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 … |
Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment |
1 |
|
2D, time-series |
ImageJ, Excel |
Software |
|
Paintera |
5.889 |
|
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 … |
ORION |
15.946 |
|
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 … |
neuTube (or NeuTu) |
10 |
|
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 … |
NeurphologyJ |
4 |
|
|
ImageJ |
Software |
… neurite attachment points Additional keywords morphometry neuron cell morphology branching Entry Curator kota Post date … |
NeuronStudio |
13.802 |
|
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 … |
NeuronMetrics |
8 |
|
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 … |
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 … … |
Neuron Tracing Vaa3D (MST) |
9 |
|
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 - … |
Neuron Tracing Vaa3D (MOST) |
8 |
|
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 (BJUT FM Spanning Tree) |
8 |
|
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 (App2) |
9 |
|
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 3D (Rivuletpy) |
9 |
|
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 3D (ImageJ) |
8 |
|
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 … |
Neurolucida |
9 |
|
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 … |
NeuroGPS-Tree |
3 |
|
3D |
Vaa3D |
Software |
|
Neuroglancer |
1 |
|
|
|
Software |
… microscopy Light-sheet microscopy has biological terms neuron skeleton Entry Curator Perrine Post date 08/07/2019 - … |
NeuroAnatomy Toolbox |
2 |
|
3D, multi-channel |
|
Software |
|
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 … |
Neural Circuit Tracer |
5.993 |
|
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 … |
NET - Network Extraction Tool |
2 |
|
2D |
|
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Thresholding … Clustering-based image … |
nctuTW |
18.641 |
|
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 … |
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 … |
MOST-Raytracer |
2 |
|
3D |
Vaa3D |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Image restoration … basic_html … … |
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 … |
MiToBo |
1 |
|
2D, 3D |
Fiji |
Software |
… has biological terms cell migration cytoskeleton neuron neurites filament Entry Curator czhang Post date … |
MicrotubuleTracker in FIJI |
2 |
|
2D, 3D, time-series |
Fiji |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … basic_html … kapoorlab … … |
Microtubules Tool (3D) |
3 |
|
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 … |
Microtubule Length Analysis |
2 |
|
2D, 3D |
Fiji, Tubeness |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Medial axis … Bioimage analysis … … |
MeasureNeurons (CellProfiler) |
6 |
|
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 … |
Measure cell volume over time |
4 |
|
3D, time-series |
ImageJ, Imaris |
Software |
|
KNOSSOS - 3D image visualization and annotation tool |
2 |
|
3D |
|
Software |
|
Junction Mapper |
2 |
|
2D, multi-channel |
|
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Feature detection … Image labeling … … |
JFilament |
3 |
|
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 … |
ImarisFilamentTracer |
2 |
|
|
Imaris, Sholl Analysis (ImageJ) |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Bioimage analysis … alban.gaignard … … |
Imaris |
4 |
|
|
Imaris |
Software |
|
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 … |
ilastik - Carving |
3 |
|
2D, 3D |
ilastik |
Software |
… Bioimage informatics Machine learning has biological terms neuron blood vessels plant tubular structure Entry Curator … |
ilastik |
1.862 |
|
2D, 3D, multi-channel, time-series |
VIGRA |
Software |
|
HyphaTracker |
2 |
|
2D, time-series |
ImageJ |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … Image pre-processing … … |
hIPNAT |
7 |
|
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 … |
Filopodyan |
2 |
|
2D, time-series |
ImageJ, Fiji |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Tracking … basic_html … Perrine … … |
Filament Tracing Tubeness (ImageJ) |
2 |
|
3D |
ImageJ, Tubeness |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Edge enhancement … Steerable fliter … … |
Filament Tracing LocThresh (ImageJ) |
2 |
|
3D |
ImageJ |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Medial axis … Bioimage analysis … … |
Filament Tracing (ImageJ) |
2 |
|
3D |
ImageJ |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Gaussian filtering … Gaussian … |
FibrilTool |
2 |
|
2D |
ImageJ |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … Manual segmentation … Slide scanner … … |
ClearMap |
2.997 |
|
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 … |
CEM |
3 |
|
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 … |
CellProfiler |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
CATMAID |
0.903 |
|
2D, 3D |
|
Software |
… Light-sheet microscopy has biological terms synapse neuron drosophila Entry Curator czhang Post date 11/07/2013 - … |
BioImage Model Zoo |
1 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… bacteria Arabidopsis ovules Arabidopsis thaliana neuron nuclei plant cell membrane stem cells vesicles … |
BioCat |
1 |
|
2D, 3D |
|
Software |
|
APP2 |
9.779 |
|
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 … |
APP (All-path pruning) |
11.634 |
|
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 … |
Angiogenesis / Sprout Analyzer (ImageJ) |
3 |
|
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 … … |
AnaMorf |
2 |
|
2D, multi-channel, time-series |
ImageJ |
Software |
… reconstruction … Curvilinear structure detection … neuron image analysis … neuron reconstruction … basic_html … vcaldas … Filament … |
Analyze Complex Roots Tool |
2 |
|
2D |
Fiji |
Software |
|
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 … |