redoing old macro

went back to preprocessing macro for tracking:

// K_SpaceEqualizer2.ijm
// attenuate the edynamic range of the image for contrast enhancing.
// started for enhancing virus+microtubule sequences.
//Kota Miura (miura@embl.de)
//050517,
//070301 modified and resavved as v2
// use algorithm2. ititially, background ROI must be defined.

IJ plugin course 2 by Cihan Cetin

a lot of practicals today:

- installing Eclipse
- making first program
- instance variables
- class variables

Elisa @ Ellenberg GE

Added a new function for

Segmented Line ROI --> Thicker Segmented Line

by combining multiple box ROIs. (measures average intensity inside)

K_SegmentedLineWidthControlv2.ijm

Mishura @ Griffith Lab Guest

Evaluate the degree of infection of certain bacteria.

I suggested to measure

Number of bacteria inside cell / Number of all bacteria

by taking two channel images, one for bacteria and other for the cytoplasm that the bacteria counting could be carried out with/without cytoplasm channel masking.

Mishura will use 96well plates for automatic capturing, so I suggested him to talk to Arne for the use of microscope. I told Mishura to comback to me when he is ready with example images.

particle tracker plugin interface

ImageJ Plugin "particle tracker" is excellent but the output text file is a bit complicated for direct use for further analysis. I made

(1) ImageJ macro to extract track data

k_ParticleTrackerOutputConverter.ijm

(2) Igor Procedure to import data processed in (1)

- importing and view all tracks
- filter out short tracks and view
* further implementation of other functions form previous track analysis Igor programs

K_particleTracker_OutPutReader.ipf

tested with Gaspar's sequence and works pretty well.

ImageJ Plugin Writing Course

Cihan yesterday did a good job for the first day of the Plugin course:
Short introduction to Java and explained how object oriented programming works.

10 people are now in the course.

Elisa @ Ellenberg GE

Elisa has task to use thicker segmented line ROI, simialr to Katherine Brown's.
So I sent Elisa the same macro freshly made some days ago.

Sib @ Cancer Research

Sib @ Michael Way's lab visited here and discussed about recent progresses on her virus studies. Some extended analysis will be done, as a continuation of those from two years ago.

particle tracker ImageJ plugin
--> output format is a bit complex
original article about this tool

Feature point tracking and trajectory analysis for video imaging in cell biology.
Sbalzarini IF, Koumoutsakos P.
J Struct Biol. 2005 Aug;151(2):182-95.