ShapeLogic 1.2 with color particle analyzer released

Here are the release notes for ShapeLogic 1.2

Changes

• Particle analyzer working directly on color and gray scale images without manual user intervention
• Both particle counter and particle analyzer now take parameters and print reports about each particle's color, area, standard deviation to result table
• Color replacer replaces one color within a tolerance with another color. Parameter input dialog with preview check box
• Organize plugins and macros under ShapeLogic? and ShapeLogicOld? menus, until 1.1 they where all placed under shapelogic menu
• ShapeLogic still has beta development status

The particle analyzer in ShapeLogic v 1.2 has gone through limited
testing and seems to work well. There is still a bug in the edge
tracer.

Using particle analyzer as a ImageJ plugin

The particle analyzer was tested on the particle sample images from ImageJ embryos.jpg

To run it from ImageJ select "Color Particle Analyzer" in the ShapeLogic? menu:

First a particle count dialog is displayed:

Here is the result of running the non-customized particle analyzer on it. This is written to a result table that can be exported to Excel:

The categories for the particles are only examples, it is easy to setup different rules for categorizing particles. In ShapeLogic? 1.3 there will be custom rules to recognize specific cells.

ShapeLogic? 1.2 also contains the second version of a color particle counter. It also prints a smaller report of the particle's properties.

Plans for next release

The next release, ShapeLogic v 1.3, will be a more mature particle analyzer which will come with custom rules to recognize specific cells.

Seeking particle images

In order to create these rules, I am looking for images of particles on a relatively uniform background. Please let me know if you have sample images that I could work from, preferably standard images like the embryo sample image that comes with ImageJ.

Possible future plans for particle analyzer

• Create rule for recognizing cells using neural networks or machine learning techniques
  
• Be able to handle a background that is not uniform, and cell organelles
• Incorporate reasoning under uncertainty using the lazy stream library
  
• Find overlapping particles and distinguish them as separate

Download ShapeLogic 1.2

-Sami Badawi
http://www.shapelogic.org

ShapeLogic 1.1 with particle counter released

Here are the release notes for ShapeLogic 1.1

Changes

• Particle counter working directly on color and gray scale images without manual user intervention
• Particle counter finds average color, standard deviation, area and location for each particle
• Framework to build more advanced particle counters and particle analyzers
• Color clustering using K-mean algorithm
• Background color finder
• Extend all the image processing algorithms in ShapeLogic to work in both ImageJ and in plain Java
• Better support for NetBeans
• ShapeLogic still has beta development status
• 29000 lines of Java code
• 440 unit test that all works on local machine

The particle counter in ShapeLogic v 1.1 has gone through limited testing, and seems to work well though tweaking the parameters is still a bit clumsy. Users looking for a mature particle counter should probably wait for ShapeLogic v 1.2.

Test on sample images from ImageJ

The particle counter was tested on the particle images from ImageJ:

embryos.jpg. The un-tweaked particle counter in ShapeLogic 1.1 found

particle count = 9

embryos.jpg contains 6 particles and a few shadows.

After changing the parameter setting it found

particle count = 5

which is the correct value since ShapeLogic 1.1 cannot split overlapping particles.

Direction

This is the first use of ShapeLogic in medical image processing. The next few releases should also be focused on the particle counter, making it more robust and automatic. This is the plan for ShapeLogic 1.2:

• More testing and tweaking of particle counter
• Make it easier to set parameters for particle counter in a macro or a configuration file
• Print report about each particle's color, area, standard deviation to a file
• Different implementations of particle counters
• Vectorize particles by tracing the edge
• Filter particles based geometric properties of the edge using the same techniques as letter matcher
  

Download ShapeLogic 1.1

-Sami Badawi
http://www.shapelogic.org