Thursday, June 28, 2007

Els@CBB

For her experiments using FRAP, we did initial experiments for determining whether the recovery can be assumed reaction dominant. For this, FRAP curves with different diameters must be tested. If the recovery curves are similar regardless of the bleaching diameter, then the curve could be considered to be "reaction dominant".

We sit together and compared several curves, with bleaching diameter small, medium or large. It seems probable for the experiment she does, that the recovery is mostly reaction dominant.

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Wednesday, June 13, 2007

Biomedical Imaging Group, EPFL

Last Friday, I was invited to EPFL for a talk at Bioimaging and optics seminar, and met with many outstanding Imaging and Optics researchers there. EPFL is located in Lausanne, a beautiful city in Switzerland.

Here is a list of people I met and talked in EPFL.

Michael Unser (Head of Biomedical Imaging Group, the BIG)

--> many excellent ImageJ Plugins they publish on the web.

Cédric Vonesch (BIG)
extremely efficient algorithm for image deconvolution.


François Aguet (BIG)
sub-pixel resolution in Z-axis.

Nathalie Garin (Head of the Microscopy-Imaging-Morphology (MIM) core facility)

--> made a tour of her huge facility!

Matthias Lutolf (Group Leader) and Stefan Kobel

--> Laboratory of Stem Cell Bioengineering
Using micropatterned wells for single stem cell culture.

Theo Lasser (Head of Laboratoire d'Optique Biomedicale)

--> many interesting new optics.
Optical Coherence Tomography OCT
Frequency Domain Optical Coherence Tomography FDOCT

Measurement of in vivo flows without labeling.


Daniel Sage (BIG)

tracking under noisy condition. (Spot Tracker)
--> seperate tracking each in X and Y.
semi-manual mode fro tracking is a great tool for interactive analysis (for Circadian Genes).

Philippe Thévenaz (BIG)

Snakuscule. A simplified SNAKE approach. Very fast.

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Tuesday, June 12, 2007

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

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Monday, June 11, 2007

MosaicJ  (from ImageJ ML)

###
#
# MosaicJ
#
# Version dated May 23, 2007
#
###

Here is a new plugin that may be useful to those of you who want to stitch together partial images so as to create a larger mosaic image.
The purpose of this plugin is to facilitate the assembly of a mosaic of overlapping individual images, or tiles. It provides a semi-automated solution where the initial rough positioning of the tiles must be performed by the user, and where the final delicate adjustments are performed by the plugin. The MosaicJ plugin requires that a second plugin, named TurboReg, is installed.

MosaicJ and its documentation is available from here:
http://bigwww.epfl.ch/thevenaz/mosaicj/

TurboReg and its documentation is available from here:
http://bigwww.epfl.ch/thevenaz/turboreg/

===
EPFL/STI/IOA/LIB/BM.4.137
P. Thévenaz
Station 17
CH-1015 Lausanne VD
===

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Monday, June 04, 2007

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

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