Plans on CMCI seminars and other things...

CMCI plans to organize intra-EMBL seminar series centered on Imaging issues. Major goal is to share information on imaging techniques and to get people be known to each other. I talked with many people who might be interested in this seminar and it seems that many people are really interested in this seminar. Since number of people is large, I started to think it might be better to do a kick-off of this seminar with a symposium, with al interested people taking in two days about their works. I talked with Jan today about this and he agrees with doing such a symposium. One of the merit is that we can then also involve the attendance of outstation scientists who might not be able to come to Heidelberg weekly. I will start setting schedule for this kick-off symposium.

- other things today-

ALMF Microscopy course is going on today, many people strolling around inside ALMF. Stefan asked me in which order one should do image subtraction and background subtraction: I wasn't sure about this. All I could show, was that in case of 32-bit results, noise actually increases its dynamic range by image subtraction so I would do backgoround subtraction first.


1. with Heiko: Cholesterol paper revising

(1) FRAP Curve fitting evaluation part, gammaQ things.
(2) Updating Frap Graphs .

2. with Darren
Darren liked the vector field analysis I did for Virginie. I gave him a pdf document explaining the optical flow estimation. We deided to collaborate.

3. Discussion with Francois
... about currently writing paper on substrate patterning.

vector field paper revising

I am (still) working on a paper about analysis of intracellualr vesicle cargo protein dynamics, or the transport of protein between different organelles, and its in the almost final form but for a year I havn't touched it (lazy guy!) . The method used is the gradient-based optical flow estimation. The paper describes about details of vesicle transport dynamics. I think that the protein sorting within cell can be described as stochastic processes, and this paper will be a primer for this purpose (I hope...).

Keyward links:
Mathworld: stochastic processes
Wikipedia: stochastic processes
Probability theory and stochastic processes

Virginie: Fish things plan

Virginie: Vec field analysis for the MT orientations. (local differences)
+ New sequences in PPK71
--> tried with the sequence 2 and clear differenc in the histogram.

Categorrizing Signals: Nucleus, Spot signals

Task: seperate three types of localization automatically:
--> same type of task appears in many applications.

A: small spots a bit remote from the nucleus
B: Large aggregate of replication sites, surrounding the nucleus.
C: diffuse cytoplasmic signal

In general, thresholding strategy will be the key for this type of problem .

Strategy:

1. Threshold DAPI at a sufficient level. (segment each cell according to nucleus)
--> do nucleus signals are always with similar intensity?
-- if not, threshold level must be set for each nucleus.
-- according to the size of nucleus?
-- dynamic thresholding --> determine the best threshold level.

2.a. Dialate Thresholded DAPI signal, to make a mask for each cell.
--> define iteration of dialate operation.
2.b. Get the centroid of the Dapi signal.
--> particle analysis

3. within the mask (=ROI), threshold to select high intensity signal.
4. count particles within the mask, get average area and intensity.

5. plotting parameters
- distance from the nucleus
- average area
- average intensity
- number of counts in graphs. (3D graph?)

--> can populations be seperated? (cluster analysis)

Heiko Collaboration, Gaspar, Fatima

1. Heiko

Making figures for a paper, which will be submitted in a short time (deadline is this weekend!).

a. Simualtion results.
b. Tracks of vesicle movements overlaid to the original frames.

for the second task, I modified Igor procedure

K_analyzeManualTracked2D.ipf

that the tracks will be color coded according to their timing.


2. Gaspar

Phototaxis things. Tracks to do circular statistics, probably will be done by 2D cross-correlation.

3. Fatima

While I was telling her how to analyze her signal, I realize that a manual for Gaussian-fit tracker must be written.