EMBL BioImage Data Analysis
EMBL BioImage Data Analysis
|"The Wolfe allows high-performance gaming, virtual reality, graphic design, and video-editing for laptops" https://t.co/aFBWBE5MQL |
About 20 hours, 7 mins ago by: Kota Miura (@cmci_)
|RT @HenriquesLab: Here's my #NanoJ and #SRRF talk in #smlms16, now in HD https://t.co/UXkdllTexK . Using @FijiSc and #opensource for live-ce… |
About 21 hours, 30 mins ago by: Kota Miura (@cmci_)
|RT @albertcardona: Bioimage analysis course on @fijisc / #ImageJ, @catmaid, @knime, #ImgLib2, #BigDataViewer, November 14-18 in Berlin. htt… |
About 3 days, 15 hours ago by: Kota Miura (@cmci_)
|@kusege_tawashy 自分でもやってみたら、400fpsの設定で500fps、900で1000の表示でした。300fps以上に設定するとかなり早めに表示されますね。一種のバグだと思います。 |
About 1 week, 5 days ago by: Kota Miura (@cmci_)
|@kusege_tawashy こんにちは。これ、実際の速度の測定はどうやっているのですか。 |
About 1 week, 6 days ago by: Kota Miura (@cmci_)
|RT @HenriquesLab: Just published #SRRF, a new #superresolution approach in @FijiSc for most microscopes https://t.co/7Cs2ktgM5z https://t.c … |
About 2 weeks ago by: Kota Miura (@cmci_)
Centre for Molecular and Cellular Imaging (CMCI)
miura at embl dot de
Tel: +49 6221 387 404
* Kota Miura et al. (2014). ImageJ Plugin CorrectBleach V2.0.2. Zenodo. 10.5281/zenodo.30769
Released under the GNU General Public License v2.
ImageJ ver 1.34j or higher (ImageJ, upgrade page).
This plugin will be a part of Fiji, so you could find it under menu tree [Image > Adjust >] in near future (as of Apr. 18, 2012).
If you want to use it in ImageJ, download CorrectBleach_.jar (right click or ctrl-click to save) and place the jar file under plugin folder of ImageJ and restart ImageJ. You will find the plugin at [Plugins → emblTool → Bleach Corrector].
This plugin contains three different methods for correcting the intensity decay due to photobleaching. They all work with either 2D or 3D time series. In case of 3D time series, image properties should be appropriately set. If you are not sure, check your image header by [Image → Properties].
This script demonstrates the headless usage.
One of our users is making timelapse experiments to track a GFP marker in cell cultures. GFP signal is very dim and background is quite strong (so SNR very poor). Over the time, background intensity decreases while specific signal keeps more or less the same so it becomes gradually more visible. He really expects the GFP to increase over the time, and he would like to quantify this increase in GFP signal over time. To compensate background bleaching he is using your bleach_corrector plugin in FIJI. He obtains the best visualization of what he expects with the Histogram Matching Method. The thing is that, as you mention in your blog's entry (http://cmci.embl.de/downloads/bleach_corrector, http://cmci.embl.de/blogtng/2010-05-06/bleach_correction_2 ), with this method you cannot quantify intensities.
Can you recommend us an alternative method to be able to quantify changes in the GFP signal over time?
Other thing is at this moment it is difficult to know is wherther everything is bleached (so GFP signal kept constant reflects an increase) or wherther bleaching affects only the medium (so GFP is really constant and is not increasing, which is not what he expects…). We will make test to address this issue…
Xavier Sanjuan (ALMU, Parc de Recerca Biomèdica de Barcelona),
on behalf of Diego Barcena (Mark Isalan group, CRG, Barcelona)
The reason histogram matching cannot be used for the measurement, to explain in your case, is because the algorithm assumes that the histogram shape is always constant (which also means that the average intensity is constant over time).
On the other hand, you know that the signal should increase if its background is constant, which means that you must assume that histogram shape does change over time, contradicting with the assumption that histogram matching is based on.
One way that I can suggest to do the correction is as follows: