Monday, July 7, 2008

ShapeLogic 1.2 with color particle analyzer released

Here are the release notes for ShapeLogic 1.2


  • 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

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