Frapcalc: V9c

-------------
Update Note (ver9c)

Mark Kwaaitaal (Max Planck Institute for Plant Breeding Research) wrote me a email pointing out that he could not see drop-down menu in the Fitpanel. I searched for the cause of problem and this defect was due to a change from IgorPro ver5 to ver6. As stated in the notes for the ver6 release

Extended syntax for PopupMenu and ValDisplay value keyword: Previously, using the # prefix meant that the following text needed to be a literal quoted string. Now, the following text can be a string expression that will be evaluated at run time to obtain the actual string expression that needs to be executed each time the popup menu is used. In other words, there is a level of indirection. (link)

and communication in email list (Link), global variable cannot be used for the command popupmenu. Only quoted string or string expression function is allowed. For this reason, following line

PopupMenu popup1,value=# G_MethodList

was replaced to

PopupMenu popup1,value=# "G_MethodList"

Two such lines were replaced.

FRAP analysis: Questions and Answers

For questions and comments, please feel free to post here in the comments section.

071030 ver9b
Stefan told me problem of negative Half Life value [s] for some cases, and I found out that when the data time range is too short and not reaching plateu, the calculation of HL results strange values. This is because HL in double exponential fitting is calculated by numerically interpolating the half max value.

To avoid this problem, estimation curve is not extrapolated that the HL becomes available even for the experiments with short time range. [now, still have problems to cope with "weighting" adjustments]

080325 ver9c
fixed popupmenu problem.
http://www.embl.org/cmci/weblog/2008/03/frapcalc-questions-and-answer-please.html

last week things shouldn't forget

-- Peter@ Surray
Made some suggestions on colocalization analysis --> improve imaging condition, such as time resolution. additionally, include MT segmentation using skeltonization routine.

-- Michael Knop
segentation of yeast shape, get long axis, measure relative position of second channel signal. Consider surface area.

Peter@Surrey lab CBB

Track microtubule end --> using the coordinates, measure the intensity at the MT tip.

For tracking

(1) Cross-Correlation
--> seems to be difficult due to large noise.

(2) Detect the position from intensity profile along microtubule.
--> edge detection

Problem with DeltaVision files: Daniela@ Griffith

When image acquisition is accidentally (or intensionally) terminated before the frame number one sets at the starting of the acquisition, the file cannot be loaded using DeltaVision Opener Plugin in ImageJ. In case of Daniela, the force-termination occurred probably due to the sudden shut-down of the server network.

I modified DVreader macro I wrote two years ago for loading these "incomplete" .dv files. Details and downloads:

http://www.embl.org/cmci/downloads/DVHeaderReader.html

Perkin Elmer data --> manual Tracking 3D

Helio @CBB requested me for making interface between

tiff 4D data series after the conversion from original Perkin Elmer data

and

format readable by manual tracker plugin for 3D tracking.

--> K_convert2MPT3D.ijm
File Converter - Perkin Elmer Tiff Series to 3D stacks
http://www.embl.org/cmci/downloads/PEfileTo3Dstacks.html

Wrapper

Cihan succeeded in wrapping C++ code and create dll for a use in JAVA. This means that C++ codes can be used as a library in ImageJ. Great achievement!

Platform: Eclipse
Compiler: gcc

Cihan will write an easy manual for this.