Kochi city - view from Godaisan.

Bridging the gap between qualitative and quantitative colocalization results in fluorescence microscopy studies.

Researchers doing fluorescence microscopy and performing quantitative colocalization analysis know how difficult it is to describe obtained quantitative data using natural language with subjective qualifiers, such as "Weak", "Moderate", "Strong", etc. Depending on what they expect, many tend to misreport their results: "Strong" colocalization in the case of overlap coefficient (standard values are from 0 to 1.0) may mean 0.99 to one researcher and 0.51 to another. This discrepancy can cause significant confusions and create errors.

For the last several years we tried to find a solution to solving this problem. Assistance came from using the fuzzy system model. With its help, we developed a tool to characterize colocalization data in a way so that they are understandable and comparable both qualitatively and quantitatively. We produced a set of just five linguistic variables tied to the values of popular colocalization coefficients: "Very Weak", "Weak", "Moderate", "Strong", and "Very Strong". The use of these variables ensures that the results of colocalization studies are properly reported, easily shared, and universally understood by all researchers working in the field. Importantly, when new coefficients are introduced, their values can be readily fitted into the set.

To make this information accessible to as many researchers as possible, we decided to publish it in Scientific Reports, an open access journal from Nature Publishing Group (NPG), so that all interested can download a free copy of the paper. Get your copy of the paper here and don't hesitate to ask if you have any questions.

"Comedians in Cars Getting Coffee" heading for Season 2!

According to the recent The New York Times report, web series Comedians in Cars Getting Coffee is heading for Season 2! This is great news for all who liked the show!

"Comedians in Cars Getting Coffee"

Just recently stumbled upon a new internet project from a sitcom superstar Jerry Seinfeld called Comedians in Cars Getting Coffee. As its name implies, its about comedians in cars getting coffee. In series of short (10 min or so long episodes) Mr. Seinfeld picks up a fellow comedian in a car and they go for lunch laughing and talking.

In many aspects it reminds of a well established British internet series Carpool, instead that, fortunately, Jerry does not drive Toyota Prius and chooses vintage cars (just two Porsches featured so far if you know what I mean) instead.

As one may expect, the first episode featured his fellow comedian and Seinfeld co-creator Larry David. The upcoming 10th episode will remind of another Seinfeld star Michael Richards (Kramer). Although not all his guests are equally sharp and entertaining, I found these little episodes a real treat to watch. Give them a try!

"Beyond the limit of histochemistry"

Poster of 14th ICHC at the entrance of Kyoto International Conference Hall.

14th International Congress of Histochemistry and Cytochemistry (ICHC) came and went and I am taking a few moments to reflect. It was my third ICHC (previous two were in Kyoto in 1996 and in Gdansk in 2008) and it is my impression that this one was probably the best in terms of both organization and attendance. Most importantly, due to recent breakthrough developments in microscopy instrumentation, the Congress was fortunate to have a common topic/theme that united many of its presentations and became a Congress key, which was super resolution. For those not very familiar, super resolution microscopes operate above the diffraction limit of light and allow to see structures at the resolution of 10 nm (compared to 220-250 nm in conventional (including confocal) fluorescence microscopes), which is nothing short of revolutionary.

   Congress started with a keynote lecture delivered by Dr. Lippincott-Schwartz from NIH. She talked about new optical probes, imaging strategies, and technical innovations. Although Congress attendees were certainly familiar that Dr. Lippincott-Schwartz is a pioneer of super resolution microscopy and more or less knew what to expect from the lecture, it was my feeling that many of them were blown away by the dynamics of the imagery she had shown and the presentation logic of her talk. I personally was impressed the most by the extent of integration of various disciplines in her studies. Researchers talk about the need for interdisciplinary approach in contemporary medico-biological science for quite some time now. But we don't see too many examples. In this case, everything was there in full bloom.

   Speaking about our workshop on quantitative methods in histochemistry and cytochemistry, we had more attendees that I expected and all three presentations went really well. We also had very lively discussions. Both Dr. Wollscheid  and Dr. Seitz are experienced and dedicated presenters and they tried to pack in their talks as much information as possible. I was glad to speak about quantification of spatial correlation of fluorescent markers mostly based on our recently published Nature Protocols paper. All three talks of us covered different areas of quantification techniques and that was the very idea of the workshop.

The next ICHC Congress will take place in Istanbul, Turkey, in 2016. I wonder what will become a key topic there?

14th International Congress of Histochemistry & Cytochemistry

From August 26th to 29th I'll be attending 14th International Congress of Histochemistry & Cytochemistry in Kyoto. This going to be my second International Histochemistry & Cytochemistry Congress in this marvelous Japanese city. First one was back in 1996, soon after I came to Japan. This time I am organizing a workshop dedicated to modern quantitative methodologies. Two outstanding European researchers working in Switzerland, Drs. Bernd Wollscheid and Arne Seitz from renown ETH Zurich and EPFL Lausanne, respectively, will be joining me at the workshop. Dr. Wollscheid will be talking about chemoproteomic technology for the ligand-based receptor identification on living cells and tissues, while Dr. Seitz will be focusing on the strategy to test fluorophores stability for typical histological samples. I will be presenting latest developments in the field of quantification of colocalization. I am glad to mention that I was able to obtain financial support for both Dr. Wollscheid's and Dr. Seitz's travel.

I am quite looking forward to the Congress, because there should be really interesting presentations there, as well as, because, as people who visited this old Japanese city even once may say, there is no any other place in the world like Kyoto.

P.S. Picture above: Kinkaku-ji (Temple of the Golden Pavilion), one of the most popular buildings in Japan and one of the World Heritage Sites.

Editorial Board of Scientific Reports

I recently joined Editorial Board of Scientific Reports, new online and open access journal from the publishers of Nature. It covers all areas of the natural sciences. As a member of Nature Publishing Group (NPG), Scientific Reports publishes technically sound, original research papers of interest to specialists within their field and without barriers to access. I am affiliated with the Cell Biology section of the Board.

To ensure rapid peer review and publication of research, Scientific Reports relies on an external Editorial Board and a streamlined peer-review system. An internal publishing team works with the board and authors to make sure that accepted manuscripts are processed for publication as quickly and smoothly as possible.

In addition, Scientific Reports leverages the tools, technology and experience of NPG to ensure that published manuscripts are enhanced by innovative web technologies. All papers are archived in PubMed Central.

I look forward to help making Scientific Reports an another NPG success.