Wednesday, February 28, 2007

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



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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.

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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.

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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.

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Monday, February 26, 2007

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.

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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.

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Friday, February 23, 2007

Adam @ Rorth lab

fragment of macro sent for dealing with splitted images after "RGB split" in imageJ.

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Marianne @ Surray lab 4: macro ver2

Modified that
- plotting is done separately, more flexible with number of traces and increments
- profile measurement is done for all frames, printed out to the result table.
- about 3hours.

K_YprojectionV2.ijm

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Carolina @ CBB Pepperkok

EM scale problem

using the scale attached to EM micrograph, same cell has different areas in different zoom (260x and 1600 x). difference is about 25% (1600x would end up in smaller appearance).

Solution is only to measure some constant scale such as grid, or beads, and plot a calibration curve for proper scales.

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Thursday, February 22, 2007

Marianne @ Surray lab 3: macro

A macro was written, to get profile along x-axis over generated mask from microtubule signal channel. Took about 4 hours.

K_Yprojection.ijm

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Janina : Fly localization 4: done for now

A macro called
K_2chCountOverlappedPixels.ijm
was made to count the overlapped dots, took about 3 hours.

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Helio @ Antony

Told how to subtract avaraged frame from a stack.

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Janina : Fly localization 3

Discussed 30 minutes and Change strategy: just count the number of overlapping dots.
--> total number of dots / brain.

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Wednesday, February 21, 2007

Marianne @ Surray lab 2

Planned for the y-axis adding up Profile mapping.

1. Thresholding
or 2. manual selection of spindle edge.

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Daniela@ Griffith

cell migration activity

--> make it simple
step1: count by category for spread cells
a. stopped
b. pivot
c. migration

step2: displacement activity
take 4 frames out of 17hrs sequence, and measure the displacement during every 5 hours.

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Carolina @ CBB

1. Scale problem: ImageJ area conversion might not be reliable (or maybe too complicated)
--> told how to convert pixel area to um2.

2. ROIs accumulated in the ROI manager are used sequentially and intensity is measured
--> requires macro programming.

3. EM scales --> zooming and scale adjustment --> this should be checked by EM people.

4. Photoshop scale:

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Katherine's analysis 2: done

continued from
http://www.embl.de/~miura/CMCI/blg/2007/02/thicker-segmented-line-roi.html#links

So the task is to measure intensity profile along segmented line ROI with certain width in perpendicular direction. a new macro was written for this:


K_SegmentedLineWidthControl.txt

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Janina : Fly localization 2

Check images from two different conditions by colocalization plugin. Initial idea to "measure the distance" between spots would be not valid since the signals are diffuse. --> design an analysis protocol by tomorrow.

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Monday, February 19, 2007

Janina : Fly localization

2 channel z-stack, trying to find the degree of colocalization.
Problem is that one signal is dotty whereas the other is diffuse.

--> compare the wild type and conditioned.
--> will discuss tomorrow again, with merged z-stacks and projections. (10 each)

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Wednesday, February 14, 2007

Celine@KnopLab

Segmentation of yeast
for Ratiometry. maybe later..

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Tuesday, February 13, 2007

Marianne @ Surray lab

Spindle fluorescence

y-direction projected intensity (integrated)
--> intensity profile along x-axis.

(don't have time so we will discuss next week)

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Martin @ Nedelec Lab

How to measure the length -severing dynamics of MT (Population, individual).
ImageJ --> use Array to label individual filaments.

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Friday, February 09, 2007

Triangulation

Jerome asked for suggestion on programming triangulation of cell positioning. He has a list of position IDs, and wants to add which of the other points are connected to that point. The number of connected point is not always same, so single position should have a flexible memory allocation.

My suggestion was to make a 2D binary matrix of Number of Positions x Number of Positions, and fill 1 for direct connections while the others 0. In this way list scanning and referencing should be fast, while the memory allocation is stably defined.

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Thursday, February 08, 2007

Thicker Segmented Line ROI

Katherine (DB) came to me asking about getting line profile suing thick -segmented line ROI. Need to test whether the thickness control is working or not: otherwise, design a macro to do that

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From now on, I try logging all the small consulting things here.

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Thursday, February 01, 2007

CMCI web page updates

- Mini symposium: Progress in Mathematical Morphology -> more information uploaded
- User list in the "Link page" added with new names.

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