Automated

DEPRECATED (as of Dec. 2018)

This plugin parses arbitrary mathematical expressions and compute results using images as variables.

This plugin combines the idea of using fiduciary markers, local descriptors and geometric hashing and applies global optimization. It can register an arbitrary number of partially overlapping point clouds. It is robust with respect to the amount of incorporated beads, bead distribution, amount of overlap, and can reliably detect non-affine disturbances (e.g. abrupt agarose movement) that might occur during imaging.

For details about the SPIM registration, fusion & deconvolution please have a look at the Multiview Reconstruction Plugin. It is much more powerful, flexible and completely integrated with the BigDataViewer.

Select a portion of a sequence in all 5 dimensions.

• Counts the number of 3D objects in a stack.
• quantifies for each found object the following parameters:
  • 3D intensity related measurement (with possible redirection to an image with the actual intensity value to be measured, for example for two channels measurements)
  • Volume and shape factors measurements, surface etc...
• generates results representations such as:
  • Objects' map;
  • Surface voxels' map;
  • Centroids' map;
  • Centres of masses' map.

As ImageJ's “Analyze Particles” function, 3D-OC also has a “redirect to” option, allowing one image to be taken as a mask to quantify intensity related parameters on a second image. But unlike the Analyze particle, it include a thresholding option, meaning that you can start from a gray level  stack, not necessarily a binary mask.

To use it, first set the list of measurements by editing 3D OC Options. Both (3D Object counter and 3D OC Options are now in the default Fiji "Analyze" menu.

This plug-in implements fast active contours for image segmentation. Their representation in terms of spline curves allows for a natural and intuitive manipulation of the active contour through control points.

Based on Delgado-Gonzalo et al. "Snakes on a Plane: A Perfect Snap for Bioimage Analysis"

Computes the distance map transform of a binary image. The distance map is a matrix which contains for each pixel the distance to its nearest background pixel.

Short Description

Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequence3', in a single step. All the operations are executed pointwise.

Documentation

This plugin is similar to the Math operations plugin: it provides usual pointwise math operations on sequences, such as addition, product, absolute value extraction, rounding to the closest integer, etc. However, it also allows the user to perform complex combinations of theses operations, using a mathematical expression interpretor.

Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. ICY plugin.