Closing

clij is an ImageJ/Fiji plugin allowing you to run GPU-accelerated code from within Fijis script editor (e.g. macro and jython). CLIJ is based on ClearCL, Imglib2 and SciJava. It contains components for image filtering, thresholding, spatial transforms, projections, binary image processing and basic signal measurements.

nctuTW is a "high-throughput computer method of reconstructing the neuronal structure of the fruit fly brain. The design philosophy of the proposed method differs from those of previous methods. We propose first to compute the 2D skeletons of a neuron in each slice of the image stack. The 3D neuronal structure is then constructed from the 2D skeletons. Biologists tend to use confocal microscopes for optimal images in a slice for human visualization; and images in two consecutive slices contain overlapped information. Consequently, a spherical object becomes oval in the image stack; that is, neurons in the image stack do not reflect the true shape of the neuron. This is the main reason we chose not to work directly on the 3D volume.

The proposed method comprises two steps. The first is the image processing step, which involves computing a set of voxels that is a superset of the 3D centerlines of the neuron. The shortest path graph algorithm then computes the centerlines. The proposed method was applied to process more than 16 000 neurons. By using a large amount of reconstructions, this study also demonstrated a result derived from the reconstructed data using the clustering technique." (Extracted from reference publication: https://doi.org/10.1371/journal.pcbi.1002658)

Illustrative image shows gold standard (top) and method results (bottom). 

Fills holes below a given threshold. 3D data is currently processed slice per slice.

Fills the holes in all the ROI of the active sequence (also works in Protocols).

Fill regions in images.