| Image registration in Matlab with Image Processing Toolbox |
32 |
|
2D, 3D, multi-channel, time-series |
Matlab Image Processing Toolbox, Matlab Computer Vision System Toolbox |
Software |
… Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image … Affine image registration … Rigid image registration … Elastic registration … Shape-based registration … |
| brainreg |
23 |
|
|
Python |
Software |
… images to be aligned in a common coordinate space. Current registration backend is niftyreg . Component of BrainGlobe … Initiative has function Alignment construction Image registration Affine registration Rigid registration Deformable registration … Affine image registration … |
| BIRL |
22 |
|
2D |
|
Software |
… BSD-3 Description BIRL stands for "Benchmark on Image Registration methods with Landmark validation". BIRL is a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The … |
| Registrationshop |
20 |
|
2D, 3D |
elastix |
Software |
… It is an interactive front-end visualization for registration software based on Elasix (VTK/ITK) has function Image registration Affine registration Rigid registration Deformable registration … Affine image registration … Rigid image registration … Elastic registration … |
| ANTs: Advanced Normalization Tools |
19.993 |
|
2D, 3D, multi-channel |
ITK |
Software |
… the statistics of brain structure and function. Image Registration Diffeomorphisms: SyN , Independent Evaluation: … (2004) (2010) , Similarity Metrics , Multivariate registration , Multiple modality analysis and statistical … (link) , DiReCT in chimpanzees has function Image registration Affine registration Rigid registration … |
| simpleElastix |
19 |
|
2D |
|
Software |
… do not know License Apache Description has function Image registration Affine registration Rigid registration has topic Multimodal imaging Additional keywords … Affine image registration … Rigid image registration … Image registration … Affine registration … Rigid registration … |
| elastix |
17 |
|
2D, 3D, multi-channel |
|
Software |
… Description Elastix is a toolbox for rigid and nonrigid registration of (medical) images. Elastix is based on the ITK library, and provides additional algorithms for image registration. The software can be run as a single-line … file that contains all relevant parameters for registration: transformation model, metric used to comapre … |
| TrakEM2 |
17 |
|
2D, 3D |
ImageJ, 3D Viewer |
Software |
… mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with … datasets. has function Alignment construction Image registration Affine registration Rigid registration Deformable registration … Affine image registration … |
| performing automatic registration for CLEM |
16 |
|
2D, 3D, multi-channel |
|
Software |
… This is an example workflow of how to perform automatic registration by - first detecting spots in both images using … non clickable. has function Alignment construction Image registration Affine registration Rigid registration Spot detection has topic … Affine image registration … |
| eC-CLEM |
14.979 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… in the web. has function Alignment construction Image registration Affine registration Rigid registration Deformable registration has topic Correlative … Affine image registration … Rigid image registration … Elastic registration … Image registration … Affine registration … |
| MSRC Registration Toolbox |
14.877 |
|
2D, multi-channel |
|
Software |
… Apache 2.0 Description This python toolbox performs registration between 2-D microscopy images from the same … works, please cite them if you use this toolbox: Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry … , 10.1021/acs.analchem.8b02885 has function Image registration Feature-based registration has topic … |
| CMTK |
13.985 |
|
2D, 3D, multi-channel |
|
Software |
… line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; … (t-tests; general linear model). has function Image registration Affine registration Deformable registration Image analysis Image … Affine image registration … |
| SPIM Registration Method (ImageJ) |
13.834 |
|
3D |
ImageJ |
Software |
… might occur during imaging. For details about the SPIM registration, fusion & deconvolution please have a look at … with the BigDataViewer . has function Feature-based registration has topic Bioimage informatics Light-sheet … 04/27/2023 - 17:10 Download Page http://fiji.sc/SPIM_Registration_Method Documentation Link … |
| ec-clem autofinder |
13 |
|
2D, 3D, multi-channel |
|
Software |
… Free and open source Description Automatic registration in 2D or 3D based on detection or binary mask. … with detections already done on it. has function Image registration Affine registration Rigid registration has topic Correlative Light … Affine image registration … |
| Fiji CMTK GUI |
13 |
|
2D, 3D |
Fiji, CMTK |
Software |
… Working version of a simple GUI frontend for CMTK image registration tools in Fiji has function Image registration Affine registration Deformable registration has topic Imaging … Affine image registration … Elastic registration … Image registration … Affine registration … |
| Correlia |
13 |
|
2D, multi-channel |
ImageJ |
Software |
… Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The … resolutions and field-of-views. has function Image registration Affine registration Deformable registration Visualisation has topic … Affine image registration … |
| BigStitcher |
11 |
|
2D, 3D, multi-channel, time-series |
ImageJ, BigDataViewer, ImgLib2 |
Software |
… samples with lightsheet microscopy. has function Image registration Affine registration Rigid registration Data handling Image deconvolution Image … Affine image registration … Rigid image registration … Image registration … Affine registration … Rigid registration … |
| BigDataViewer |
11 |
|
2D, 3D, multi-channel, time-series |
ImgLib2 |
Software |
… Fiji's SPIMage processing pipeline. has function Image registration Affine registration Rigid registration Visualisation Image visualisation has topic … Affine image registration … Rigid image registration … Image registration … Affine registration … Rigid registration … |
| Multiview Reconstruction |
11 |
|
3D, multi-channel, time-series |
BigDataViewer, ImageJ, ImgLib2 |
Software |
… timeseries or multicolor stacks. has function Image registration Affine registration Rigid registration Affine transformation Chromatic aberration … Affine image registration … Rigid image registration … Image registration … Affine registration … Rigid registration … |
| pystackreg |
11 |
|
2D, 3D |
StackReg, TurboReg |
Software |
… frame. has function Alignment construction Image registration Affine registration Rigid registration has topic Electron microscopy Fluorescence … Affine image registration … Rigid image registration … Image registration … Affine registration … Rigid registration … |
| DeepCLEM |
10.7 |
|
2D |
Fiji, Register Virtual Stack Slices (Fiji), CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji |
Software |
… Description This Fiji plugin is a python script for CLEM registration using deep learning, but it could be applied in … also provided to train an new model, based on CSBDeep. The registration is then performed as a feature based registration, using register virtual stack plugin (which … |
| FNIRT |
10 |
|
2D |
FMRIB's Linear Image Registration Tool FLIRT |
Software |
… Group, FMRIB, Oxford, UK Requires FMRIB's Linear Image Registration Tool FLIRT Execution Platform Unsure … License/Openness I do not know Description Non linear registration intensity based for MRI brain exams. To be applied after FLIRT has function Image registration Deformable registration has topic Magnetic … |
| FMRIB's Linear Image Registration Tool FLIRT |
9 |
|
2D |
|
Software |
… I do not know Description FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate … for linear (affine) intra- and inter-modal brain image registration. FLIRT comes with a main GUI as well as three … for concatenating saved transformations has function Image registration Linear transformation has topic Magnetic … |
| Automated workflow for parallel Multiview Reconstruction |
9 |
|
3D, multi-channel, time-series |
Fiji, Snakemake |
Software |
… cluster or on a single workstation. has function Image registration Image deconvolution Selective plane illumination … Image registration … |
| FreeD |
9 |
|
2D, 3D |
Segmentation of Clustered Cells in MATLAB |
Software |
… Bourgin, INRA Versailles, France. has function Deformable registration Feature-based registration Image segmentation Analysis Clustering has topic … Elastic registration … Shape-based registration … Object registration … Deformable registration … Feature-based registration … |
| Bigwarp |
8 |
|
2D, 3D, multi-channel |
|
Software |
… deformation from point correspondences. has function Image registration Deformable registration Warping has topic Correlative Light and Electron … Reference Publication Link Bogovic et al Robust registration of calcium images by learned contrast synthes… … Elastic registration … |
| SPIM Bead Registration |
8 |
|
|
ImageJ |
Software |
… Free and open source has function Feature-based registration has topic Light-sheet microscopy Entry Curator … 04/27/2023 - 16:50 Download Page http://fiji.sc/SPIM_Bead_Registration_(deprecated) Backlinks … Shape-based registration … Object registration … Feature-based registration … |
| TeraStitcher |
7 |
|
2D, 3D, multi-channel |
|
Software |
… ) and processed. has function Alignment construction Image registration Rigid registration Image stitching Post date 01/30/2018 - 09:40 … Rigid image registration … Image registration … Rigid registration … |
| ViBE-Z |
7 |
|
3D |
|
Software |
… the right input data and format. has function Image registration Deformable registration has topic Bioimage informatics Confocal … Elastic registration … Image registration … Deformable registration … |
| StackReg |
7 |
|
3D, time-series |
ImageJ, TurboReg |
Software |
… of image slices. has function Alignment construction Image registration Rigid registration has topic Live sample imaging Electron … Rigid image registration … Image registration … Rigid registration … |
| ABBA |
6.993 |
|
2D |
ImageJ |
Software |
… atlases. ABBA is available as a Fiji plugin for performing registration; a QuPath extension is also available and … as a QuPath project, that is registered within Fiji. The registration results can then imported back into QuPath for … may also access all BrainGlobe atlases. has function Image registration has biological terms brain Additional keywords … |
| iterative closest point registration |
6 |
|
|
|
Software |
… functions, edge point rejection, etc. has function Rigid registration has topic Bioimage informatics Post date … Rigid image registration … Rigid registration … iterative closest point registration … |
| Manual Frame Drift Registration |
6 |
|
2D, time-series |
ImageJ, Manual Tracking ImageJ |
Software |
… Free and open source Description has function Image registration Drift correction Image correction has topic … Image registration … Manual Frame Drift Registration … |
| BUnwarpJ |
6 |
|
2D |
ImageJ |
Software |
… License/Openness Free and open source Description 2D Image registration method based on elastic deformations represented by B-splines. has function Deformable registration Warping has topic Bioimage informatics … Elastic registration … Deformable registration … 2D Image registration method based on elastic deformations represented … |
| Intramodal registration software |
6 |
|
2D |
|
Software |
… License/Openness Free and open source has function Image registration has topic Bioimage informatics Entry Curator … - 11:59 Download Page http://bigwww.epfl.ch/thevenaz/registration/ Backlinks … Image registration … Intramodal registration software … |
| CellProfiler Align |
5.953 |
|
2D |
CellProfiler |
Software |
… Free and open source Description has function Rigid registration Entry Curator migration Post date 10/15/2013 - … Rigid image registration … Rigid registration … |
| Correct 3D drift |
5 |
|
2D, 3D, time-series |
|
Software |
… Free and open source License GPLv3 Description Rigid registration of time series in 3D. A video tutorial is … ) has function Image registration has topic Live sample imaging Fluorescence … Image registration … Rigid registration of time series in 3D. A video tutorial is … |
| OpenCV feature2d module |
5 |
|
2D |
OpenCV |
Software |
… and open source License BSD has function Feature-based registration Image analysis Image feature detection Object … Shape-based registration … Object registration … Feature-based registration … |
| Template Matching and Slice Alignment--- ImageJ Plugins |
5 |
|
2D, time-series |
ImageJ, OpenCV |
Software |
… stack utilized the previous matching function to do slice registration(alignment) based on a selected landmark. For … cvMatch_Template Align Slices in Stack has function Image registration Post date 05/07/2018 - 19:01 Last modified … Image registration … stack utilized the previous matching function to do slice registration(alignment) based on a selected landmark. For … |
| Align slices in stack |
5 |
|
2D, time-series |
ImageJ |
Software |
… open source License GPLv3 Description has function Image registration Additional keywords drift correction Post date … Image registration … |
| Render |
5 |
|
2D |
ImgLib2 |
Software |
… has function Alignment construction Feature-based registration Object feature extraction Data handling Image … Shape-based registration … Object registration … Feature-based registration … |
| ClearMap |
5 |
|
3D, multi-channel |
OpenCV, scikit-image |
Software |
… 3.0 Description ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues. It was … or samples. has function Alignment construction Image registration Image analysis Filament tracing Cell … Image registration … ClearMap is a toolbox for the analysis and registration of volumetric data from cleared tissues. It was … |
| Register Virtual Stack Slices (ImageJ) |
5 |
|
2D, 3D |
ImageJ |
Software |
… remain intact. The plugin can perform 6 types of image registration techniques: - Translation - Rigid (translation + … automatically extracted SIFT features. has function Image registration has topic Bioimage informatics Additional … Image registration … remain intact. The plugin can perform 6 types of image registration techniques: - Translation - Rigid (translation + … |
| Register Virtual Stack Slices (Fiji) |
5 |
|
3D, time-series |
Fiji |
Software |
… open source License GPLv3 Description has function Image registration has topic Bioimage informatics Additional … Image registration … |
| UnwarpJ |
5 |
|
|
ImageJ |
Software |
… Free and open source has function Deformable registration has topic Bioimage informatics Entry Curator … Reference Publication Link Elastic Registration of Biological Images Using Vector-Spline … Elastic registration … Deformable registration … |
| 3D segmentation (reconstruction) and modeling using Free-D |
4.993 |
|
2D, 3D |
|
Software |
… 3d stacks * (optional for serial sections) perform a 2D registration to align image slices * segment/reconstruct 3D … contours is on the software's TODO list has function Image registration Analysis Image segmentation Additional keywords … Image registration … |
| 2D brain slice region annotation: SliceMap |
4.985 |
|
2D |
|
Software |
… the reference slices to the sample slice (using elastic registration plugin BUnwarpJ) and uses the resulting image … has function Image registration Image segmentation has topic Widefield … Image registration … the reference slices to the sample slice (using elastic registration plugin BUnwarpJ) and uses the resulting image … |
| Vaa3D |
4.88 |
|
2D, 3D, multi-channel, time-series |
Vaa3D, ITK, ICY Annotation, 3D Viewer |
Software |
… image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and … platform, possibly within minutes! has function Image registration Cell segmentation Annotation Data handling … Image registration … image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and … |
| StabiTissue |
4 |
|
3D |
Python |
Software |
… stabilized images in a new folder 2701 has function Rigid registration has topic Bioimage informatics Entry Curator … Rigid image registration … Rigid registration … |
| Resolving the process of Clathrin mediated endocytosis using Correlative Light & Electron Microscopy (CLEM) |
4 |
|
|
|
Software |
… License/Openness Commercial Description Multimodal image registration based on manual selection of matching pairs of landmarks. This image registration workflow is based on MATLAB’s image processing … Multimodal image registration based on manual selection of matching pairs … |
| The Visualisation Tooklit (VTK) |
4 |
|
2D, 3D, time-series |
|
Software |
… academic, and research communities. has function Rigid registration Image thresholding Visualisation Image … Rigid image registration … Rigid registration … |
| Transform Virtual Stack Slices |
4 |
|
3D |
ImageJ |
Software |
… License/Openness Free and open source has function Rigid registration Geometrical transformation has topic Bioimage … Rigid image registration … Rigid registration … |
| ImageJ Align RGB planes |
3.973 |
|
2D |
ImageJ, EBImage rotate, CellProfiler Align |
Software |
… window, but use those buttons instead." has function Rigid registration Rotation Chromatic aberration correction … Rigid image registration … Rigid registration … |
| u-track |
3.854 |
|
2D, 3D, time-series |
Matlab Image Processing Toolbox, Bio-Formats |
Software |
… fluorescently-labeled cell nuclei. has function Affine registration Cell tracking Particle tracking Visualisation … Affine image registration … Affine registration … |
| MultiStackReg |
3 |
|
3D |
Fiji, TurboReg |
Software |
… two stacks. has function Alignment construction Image registration has topic Imaging Electron microscopy Light … Image registration … |
| Morpholeaf |
3 |
|
|
FreeD |
Software |
… and Development group at RDP, Lyon. has function Image registration Image feature detection has topic Bioimage … Image registration … |
| Amira |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… to neuroscience and bioengineering. " has function Image registration Analysis Visualisation has topic Multimodal … Image registration … |
| MIPAV |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… monitor, and treat medical disorders. has function Image registration Image analysis Object-based colocalisation Image … Image registration … |
| Spark Stitcher |
3 |
|
3D, multi-channel |
Fiji |
Software |
… Fiji https://github.com/fiji/Stitching has function Image registration Illumination correction Image stitching has … Image registration … |
| Cancer Imaging Phenomics Toolkit (CaPTk) |
3 |
|
2D, 3D |
|
Software |
… mechanisms of cancer development. has function Image registration Image analysis Image segmentation Object feature … Image registration … |
| simpleITK |
3 |
|
2D, 3D |
|
Software |
… towards supporting R packaging. has function Image registration Image analysis Image segmentation Data handling … Image registration … |
| MeVisLab |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… open source Free but not open source has function Image registration Image segmentation Morphological operation … Image registration … |
| NanoJ |
3 |
|
2D, 3D |
ImageJ |
Software |
… Tools for super resolution microscopy has function Image registration Image analysis Image processing Image correction … Image registration … |
| pyBPDL |
3 |
|
2D |
Python |
Software |
… activations in a time domain, etc. has function Image registration Image analysis Shape features has biological … Image registration … |
| Epina Image Lab |
3 |
|
2D |
|
Software |
… color photos. has function Alignment construction Image registration Image analysis Image processing has topic … Image registration … |
| QuantiFish |
3 |
|
2D |
|
Software |
… fluorescence throughout the specimen. has function Image registration Image thresholding Object counting Object … Image registration … |
| Fast4DReg |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… suffer from a misalignment of channels. has function Image registration has topic Live sample imaging Fluorescence … Image registration … |
| Image Stabilizer |
3 |
|
2D, time-series |
ImageJ |
Software |
… Free and open source Description has function Image registration Additional keywords Optical Flow Lucas-Kanade … Image registration … |
| KNIME align image |
3 |
|
2D |
KNIME |
Software |
… in KNIME Image Processing extension has function Image registration has topic Bioimage informatics Additional … Image registration … |
| Align Image by line ROI |
3 |
|
2D |
Fiji |
Software |
… line ROIs and align two images. has function Image registration has topic Bioimage informatics Entry Curator … Image registration … |
| Elastic Alignment and Montage |
3 |
|
2D |
Fiji |
Software |
… Free and open source Description has function Image registration Image stitching has topic Bioimage informatics … Image registration … |
| Landmark Correspondences |
3 |
|
2D |
ImageJ, Fiji |
Software |
… Squares fit for the available models. has function Image registration Geometrical transformation has topic Imaging … Image registration … |
| TurboReg |
3 |
|
|
ImageJ |
Software |
… and the other the target image. has function Image registration has topic Imaging Entry Curator lplantard Post … Image registration … |
| ITK |
3 |
|
2D, 3D, multi-channel, time-series |
|
Software |
… end users without development skills has function Image registration Image analysis Image segmentation Image … Image registration … |
| Relate |
2.989 |
|
2D, 3D, multi-channel |
|
Software |
… analytical data to text or CSV files has function Image registration Image analysis Image segmentation Particle … Image registration … |
| Imaris |
2.938 |
|
|
Imaris |
Software |
… data visualization (hundreds of GB) has function Image registration Object detection Object tracking Visualisation … Image registration … |
| MIA |
2.87 |
|
2D, 3D, multi-channel, time-series |
Fiji, MorphoLibJ |
Software |
… Facility at the University of Bristol. has function Image registration Image analysis Image segmentation Object … Image registration … |
| Measure cell volume over time |
2.839 |
|
3D, time-series |
ImageJ, Imaris |
Software |
… 3. Correction of shift between the time frames by rigid registration [imagJ macro] 4. Bleaching correction [imageJ … Documentation Link This Page DOI link registration_and_bleaching_correction: initial resease … 3. Correction of shift between the time frames by rigid registration [imagJ macro] 4. Bleaching correction [imageJ … |
| MetroloJ |
2 |
|
2D, 3D, multi-channel |
ImageJ |
Software |
… and finally the characterization of its spectral registration. has function Image validation has topic … and finally the characterization of its spectral registration. … |
| Lama: The LocAlization Microscopy Analyzer |
2 |
|
2D, multi-channel |
|
Software |
… analysis, localization precision estimation and image registration. LAMA works with a graphical user interface … analysis, localization precision estimation and image registration. LAMA works with a graphical user interface … |
| BraiAn |
2 |
|
2D, multi-channel |
QuPath, Python |
Software |
… obtained in whole-brain imaging experiments, following registration to an atlas. The package consists of two … obtained in whole-brain imaging experiments, following registration to an atlas. The package consists of two … |
| 3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM) |
2 |
|
|
|
Software |
… 1. Bias correction for inhomogene lighting 2. Image registration of TEM sections / stacks 3. Detection of … 1. Bias correction for inhomogene lighting 2. Image registration of TEM sections / stacks 3. Detection of … |
| Analyze 12.0 |
2 |
|
|
|
Software |
|
| Image Stitching Fiji |
2 |
|
2D, 3D, multi-channel, time-series |
Fiji |
Software |
… an arbitrary amount of channels and supports timelapse registration. To remove brightness differences at the tile … an arbitrary amount of channels and supports timelapse registration. To remove brightness differences at the tile … |
| Snakemake |
1 |
|
|
|
Software |
|
| FARSIGHT |
1 |
|
|
Segmentation of Clustered Cells in MATLAB |
Software |
… cell tracing, cell tracking, and vessel tracing. Registration and mosaicing algorithms for large scale … cell tracing, cell tracking, and vessel tracing. Registration and mosaicing algorithms for large scale … |
| Schnitzcells |
1 |
|
2D, time-series |
MATLAB |
Software |
… License/Openness Free and open source License GPL (registration required) Description Schnitzcells is a MATLAB … |
| OpenCL |
0.989 |
|
2D, 3D, multi-channel, time-series |
|
Software |
|
