Bioimage informatics

When trying to isolate objects, one strategy might be to use regular morphological operations (opening/closing) to remove small objects that are not of interest. In case small objects are made of a large number of pixels, this operation might impair the remaining objects' contours. An alternative strategy might be to use morphological reconstruction. In short, seed is placed on the image, on objects, then conditional dilation is performed from those seeds.

Here is how to proceed, using MorphoLibJ:

1. Open an image
2. Use the multi-point selection tool and place seeds on objects of interest
3. Create a new image of same size, black background
4. Transfer the selection to the new image (Edit/Selection/Restore selection)
5. Draw (make sure you're using white foreground) the multiple point selection
6. Launch the Morphological reconstruction plugin: Plugins > MorphoLibJ > Morphological reconstruction

neuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.

to be completed

The ICP algorithm takes two point clouds as an input and return the rigid transformation (rotation matrix R and translation vector T), that best aligns the point clouds. Example: [R,T] = icp(q,p,10); Aligns the points of p to the points q with 10 iterations of the algorithm. The transformation is then applied using R*p + repmat(T,1,length(p)); The file has implemented both point to point and point to plane as well as a couple of other features such as extrapolation, weighting functions, edge point rejection, etc.

This plugin applies the Hough Transform for Circles to an 8-Bit image, shows the resulting Hough Space in a new window and marks the centers of the found circles.