Wednesday, May 23, 2007

great software for cluster analysis

Weka 3: Data Mining Software in Java


Elisa @ Ellenberg GE

made some suggestions on how to set up semi-automatic macro for

saving tracking results as text files.
re-loading track coordinates from text files.
manual assignment of linking information from different channels

--> and my assignment is to give her some fragments of functions for this.


Gaspar DB

Made some suggestions on analyzing spatial distribution of embryo and its changes over time. (modify "diffusion with drift" theory).
--> plan to write down the theory and protocol for the fitting.

Friday, May 11, 2007

Guillaume @ CBB

Guillaume asked me for advise on quantification of signals. We made some "dream analysis and results" scheme. For three dimensional stack, intensity measurement should be done knowing how z-slice thickness is compared to the z-stepping distance. Numerical aperture, object magnification limits the theoretical thickness of the optical section so this should be kept in mind when taking images for the quantification.


course finished

I just now finished image processing course that continued three weeks in a row. I called for the participants in November 2006 and all the people in the list is now done. Next call will be in a month for both basic and intermediate courses.

Thursday, May 03, 2007

things done today

  1. send abstract of my talk in June in EPFL, Lausanne
  2. organizing the basic course next week
  3. advertising the CMCI seminar tomorrow
  4. Converting the tutorial slides for the workshop this week to Flash .swf


Wednesday, May 02, 2007

cygwin x / start up imageJ

1. start up cygwin, then
2. type in
ssh -X username@host
3. then start imageJ
e.g. /usr/local/bin/imagej_run