Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. The clustering is done with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.

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KNIME workflow to visualize a dataset described by multiple quantitative features (ex: a list of samples or cells, each described with multiple morphological features) as a 3D cloud of points (each point corresponding to one sample/cell) as well as a line plot (1 line per sample/cell).

For the 3D plot, the workflow uses Principal Component Analysis (PCA) for dimensionality reduction, ie it simplifies the information for each sample from n-features to 3 pseudo-features which are used as x,y,z-coordinates for each sample.

The workflow is interactive and so selecting in one panel of the figure will highlight in the other panel too.

It was originally published for the visualization of phenotypic kidney features in zebrafish, but the workflow is generic by design and can be reused for any quantitative feature set. 

Just make sure that the PCA represents a decent % of the original data variance (at least 70%). Otherwise the PCA plot will not be representative of the original data-distribution.


The Topology ToolKit (TTK) is an open-source library and software collection for topological data analysis in scientific visualization.

TTK can handle scalar data defined either on regular grids or triangulations, either in 2D or in 3D. It provides a substantial collection of generic, efficient and robust implementations of key algorithms in topological data analysis. It includes:
 · For scalar data: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, topological simplification;
 · For bivariate scalar data: fibers, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces;
 · For uncertain scalar data: mandatory critical points;
 · For time-varying scalar data: critical point tracking;
 · For high-dimensional / point cloud data: dimension reduction;
 · and more!


TTK makes topological data analysis accessible to end users thanks to easy-to-use plugins for the visualization front end ParaView. Thanks to ParaView, TTK supports a variety of input data formats.

TTK is written in C++ but comes with a variety of bindings (VTK/C++, Python) and standalone command-line programs. It is modular and easy to extend. We have specifically developed it such that you can easily write your own data analysis tools as TTK modules.

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This R package implements the NBLAST neuron similarity algorithm described in a preprint available at In addition to basic pairwise comparison, the package implements search of databases of neurons. There is also suport for all x all comparison for a group of neurons. This can produce a distance matrix suitable for hierarchical clustering, which is also implemented in the package.

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