gitlab.pasteur.fr / bia 175 Repositories
The bioimage analysis unit projects
bia/icy/extensions/opencv
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/icy/icy
Icy is an open community platform for bioimage informatics
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0
bia/parent-pom-base
Common parent POM for all Icy related projects
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/track-intensity-profile
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/intensity-projection
Intensity projection plugin. It does intensity project along depth or time with multiple algorithms: mean, max, median, variance, standard deviation, saturated sum. Projection can also be restricted to ROI.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/track-instant-speed
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/texture-segmentation
It is a toy plugin to test semi-supervised texture segmentation using the new SLBPriu texture descriptor.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/slic
SLIC: Simple Linear Iterative Clustering An Icy plugin implementing this popular segmentation technique
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-proximty-analysis
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-intensify-evolution
Compute and display the intensity evolution for regions of interests (ROIs) through time. Results can be refreshed automatically as ROIs are changed.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-inclusion-analysis
ROI Inclusion Analysis plugin for Icy.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/path-intensity-profil
Compute the intensity profile of ROI contour along Z (3D) and T (timelaps) dimension. Generates a workbook document containing all the intensity values for each point of the contour, can be plotted as graph or exported as CSV
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/nherve-image-analysis
A toolbox to chain image analysis processes
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/nherve-toolbox
My own toolbox used for all the plugins I developed.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/msd-track-processor
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/track-motion-profiler
Track Motion Profiler plugin for Icy. This plugin adds Motion Profiler and Motion Filter processors to Track Manager.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/icy-median-filter
Icy plugin for applying median filter on 2D and 3D sequences
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/plugin-template
Template to create new Icy plugin (POM file and base plugin class)
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1
bia/kmeans-color-quantization
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/mask-editor
This plugin is designed to manipulate binary masks over images. It contains all the basic tools to manage such objects.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/icy-random-roi-coloring
A simple plugin to randomly assign colors to ROIs in sequences. Also available for protocols
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/global-visible-persistence
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/distance-transforms
Distance Transforms Plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/distance-profiler-processor
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/color-track-processor
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/track-processor-excel-export
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/active-contour
Active Contours plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/roi-statistics
ROI Statistics plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/color-picker-threshold
Image segmentation by representative colors selection. Two versions are available : – thresholding – positive and negative colors selection and SVM learning
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/spot-detector-block
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/tracking-benchmark-generator
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/track-manager
Track Manager plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/spot-tracking-blocks
Spot Tracking Blocks plugin for Icy. This plugin brings Spot Tracking tools into Protocols (Graphical Programming)
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-block
ROI blocks plugin for Icy. This plugin deliver a set of ROI tools to be used with Protocols (Graphical Programming).
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/workbooks
Toolbox to create and manipulate result tables with plug-ins and protocols, and export as text file or to your favorite spreadsheet software
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/convexify
Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/sequence-blocks
Sequence blocks plugin for Icy. This plugin deliver a set of Sequence tools to be used with Protocols (Graphical Programming).
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/spot-detector
Spot detector plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/spot-tracking
Spot Tracking plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/linear-programming
A open-source utility library for linear programming in Java with the simplex algorithm.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-tagger
Create a list of tag and apply them to ROIs.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/roi-pool
Manage a list of ROIs that the user can store and pop back in one click.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/micro-manager-blocks
Blocks (Protocols) for Micro-Manager plugin
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/micro-manager-for-icy
Micro-Manager plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/blockvars
This project contains icy utilitary var classes to help protocol creation.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/rigid-registration
A simple tool to correct chromatic shifts as well as temporal drift (including translations and rotations), based on spectral correlation.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/nherve-matrix
A patched version of the Jama library. Internal structures accessors and package name added. The original version can be found here : http://math.nist.gov/javanumerics/jama/
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/jna-library-for-icy
The Java Native Access (JNA) library for Icy https://github.com/java-native-access/jna
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/connected-components
This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploi
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/color-bar
Display the colormap over the image using an overlay.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/rsyntaxtextarea-for-icy
RSyntaxTextArea library for Icy. Badically it provides a TextArea component with syntax highlight for different languages.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/jep
Embed CPython in Java through JNI
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/hk-means
HK-Means plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/label-extractor
Extracts labeled objects from a binary or labeled image into ROI using connected component analysis
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/icy-fillholesinroi
Icy plugin for filling holes on ROIs
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/spot-detection-utilities
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/jama-for-icy
Jama Matrix Package library for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/java3d-for-icy
Java3D library for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/3d-mesh-roi
SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume) meshes.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/quickhull
QuickHull library for Icy. Computes convex envelopes of random point sets in 2D or 3D.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/vecmath
Provides 3D vector mathematics classes.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bia/icy-bioformats
Bio-Formats library patched for Icy. The patch consist of replacing Apache Commons IO library by a newer version and also replacing org.json library with the custom version embedded into Micro-Manager to make it work properly.
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
bia/protocols
Protocols (GUI part) plugin for Icy
Last synced at: 7 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
