Kochi City Scape

View from the castle. Lens: AF-S DX NIKKOR 18-55mm f/3.5-5.6G VR. Stitched with Adobe Photoshop. Enhanced with Apple Aperture.

Sakura

Lens: AF-S DX NIKKOR 35mm f/1.8G.

Colocalization and cancer cells

A rapidly growing evidence suggests the possibility of the link between changes of the degree of colocalization of various antigens in the cells and the spectrum of their malignant properties. This is hardly surprising, since it has been known for a long time that various proteins are overexpressed in cancers. Discordant overexpression of colocalized proteins should inevitably result in the shift of their colocalization properties.

A recent study that caught my attention described overexpression of adenylate cyclase-associated protein 1 (CAP1) in pancreatic cancers. Fluorescence microscopy showed colocalization of CAP1 with actin to the edge of lamellipodia. Knockdown of CAP1 by the RNA interference technique resulted in the reduction of lamellipodia formation, hence colocalization as well, and motility and invasion properties of pancreatic cancer cells. Interestingly, the authors concluded that this is the first report that demonstrated the overexpression of CAP1 in pancreatic cancer cells and suggested the involvement of CAP1 in their aggressive behavior. Thus, the described observation of colocalization of CAP1 with actin served to identify CAP1 as a marker for this type of cancer as well as determined its usefulness for prognosis. Since quantification of colocalization not only proves its existence objectively, but also provides many important additional details about it (dynamical changes, contribution to colocalization of a particular antigen/channel, etc.), it is natural to expect that the use of this methodology should significantly extend the significance of these and similar observations by making them less descriptive and much more factually-based. In addition to the peripheral proteins, it can be expected that changes of the degree of colocalization can have diagnostic and prognostic values when examined in the nuclei of tumor cells, such as for example colocalization of promyelocytic leukemia (PML) bodies with telomeres (Cancer Res 2007;67:7072).

It should be mentioned, however, that the use of quantification requires a certain level of methodological knowledge and skills to ensure that it is executed correctly. It is also critical to ensure that images for analysis are properly acquired and processed prior to quantification. Fortunately, this issue received a much required attention of late with the appearance of several high quality articles stressing the importance of accuracy and precision in quantitative fluorescence microscopy and even describing a specialized quantitative colocalization analysis protocol. An another important thing worth noting is that, to be actually useful for diagnostics, quantification of colocalization should be at least semi-automated. This can be addressed by employing the latest software tools when, for example, the whole workflow of image analysis is saved as a preset or even as an action (similar to the Photoshop action), which then can be re-used and re-applied easily and quickly on as many images as needed. The critical issue here is to ensure that all images are prepared for the analysis and then analyzed in exactly the same fashion so that the results of calculations are easily reproduceable and fully comparable.

To conclude, we will likely see a noticeable increase in the number of studies attempting to use quantification of colocalization in tumors for diagnostic and prognostic purposes in the near future. Lets hope they adhere to the methodological guidelines and report really promising and applicable observations.

Haiti Indie Relief

CoLocalization Research Software will be participating in the Indie Relief effort to gather money for Haiti earthquake victims. Indie Relief will take place on January 20th: http://www.indierelief.com/.

CoLocalizer Express and Macnification combine forces

CoLocalization Research Software and Orbicule joined forces to offer CoLocalizer Express and Macnification in a bundle. The bundle combines two of the best applications for analysis of microscopy images created for the Macintosh platform. It is also an excellent match in terms of the applications' features, reliability, and ease of use.

Importantly, the bundle is offered at a very affordable price. For a limited time, the licenses of both applications can be purchased for an amazing EUR 199. That's a saving of EUR 30!

Macnification, CoLocalizer's good companion

In addition to quantifying colocalization, you can also asses other morphological parameters of your images, such as to measure and analyze the size of the cells and their different components. This comes in very handy to properly understand the significance of colocalization calculations. The best way to perform these types of measurements it is to use Macnification, a scientific application for organizing, editing, and analyzing of medico-biological imagery. Macnification lets you create folders where you can store your images, analyze them, and master image meta data. It also handles microscopic images in the variety of specialized file formats.

It is worth mentioning that Macnification is a 2008 Mac Design Award Winner for Best Mac OS X User Experience. As can be expected, it provides outstanding look and feel of the best breed of Macintosh software and guarantees an exquisite user experience.

Tuscany: Panorama of Florence

Tuscany: Pisa

Tuscany: Villas

Tuscany: Bachus

Tuscany: Wine Grapes

Tuscany: Lucca

Tuscany: Panorama of Lucca

Tuscany: Hills

CoLocalizer Pro 2.5.1 is an Apple.com Staff Pick

For those visiting Math & Science page of Apple.com, there is an information about CoLocalizer Pro. Apple.com classified it as a Staff Pick.

Colocalization? No, false presentation

I recently came across an article in the Journal of Cell Biology (JCB) entitled "Quantitative proteomics identifies a Dab2/integrin module regulating cell migration" (JCB 2009; 186:99–111). Finding images with colocalization in it, I expected them to be analyzed quantitatively as well. That was a wishful thinking. On Figure 5 of the article, Teckchandani et al. counted the number of colocalized and non-colocalized particles of Dab2 an integrinbeta1 and made conclusions about their ratio in ventral versus dorsal surfaces. How they determined coloalized particles? Visually. Non-colocalized ones? Also visually. How did they compare them? Visually as well! What a visual (and totally erroneous) approach! Ironically, the paper uses word "quantitative" in the title. But that is not for quantifying colocalization, that's for other things. Why? This is a good question.

Replying to my inquiry, Dr. Cooper of Fred Hutchinson Cancer Research Center shared a truly contemporary and very scientific attiude by saying that he believes only in what he sees and never relies on a "clever computer stuff". Is this disbelief applicable to the mentioned above paper he co-authored as well?

It is known that JCB not only sets trends in cell and molecular biological research, but also devotes a meaningful portion of its pages to the articles describing how to interpret and analyze biological imagery. It also explains the benefits of quantification of data and encourages readers to use it in their research. Worth mentioning in this regard are "Seeing is believing?" (JCB 2006; 172:9-18) and a very recent "Accuracy and precision in quantitative fluorescence microscopy" (JCB 2009; 185:1135-1148). So why JCB published a paper that ignores its own policies? This is an another good question.

Conclusion? Some people who publish their efforts in JCB should probably read the journal as well ... or choose a less visible venue for their misguiding publications.

New review came out

We have written a new review "Recent advances in quantitative colocalization analysis: focus on neuroscience" for "Progress in Histochemistry and Cytochemistry". The review summarizes latest information about applications of quantitative colocalization in the field of neuroscience.

Many thanks to the authors of excellent cited papers with whom we discussed their findings during preparation of the manuscript.

CoLocalization Research Software releases CoLocalizer Pro 2.5

CoLocalization Research Software released CoLocalizer Pro 2.5, a major update to its popular scientific imaging application. CoLocalizer Pro is now used by leading research organizations worldwide. Its customers work in various scientific and commercial institutions. Among them are Genentech, Nestle Corporation, as well as distinguished research laboratories at Harvard University, UC Berkeley, MIT, Columbia University, UC San Diego, UCLA School of Medicine, La Jolla Institute of Molecular Medicine, Mount Sinai School of Medicine, McGill University, University of Tokyo, and many others.

This update adds more viewing capabilities, improves check for update functionality, and introduces a very elegant personalized licensing feature. It is free to all users of CoLocalizer Pro 2.0. Users of earlier versions can upgrade for a fee.

The update can be downloaded here. For more details visit the site of CoLocalization Research Software.

MacResearch praises CoLocalizer Pro

MacResearch, a website dedicated to the use of Macs in research, posted CoLocalizer Pro software review.

The review describes the purpose of using CoLocalizer Pro in medico-biological field and explains why it is significantly better than any other types of software that can count colocalization. In particular, it is clarified that using confocal images for quantitative colocalization analysis without corrected background usually results in overestimation of colocalization.

Description of software is very informative yet very concise. The review is a remarkably useful bit of knowledge for all researchers who obtain and analyze confocal images with colocalization.

Quantitative Colocalization Analysis Protocol

Current Protocols in Cell Biology, the best and the most popular compilation of protocols in cell biology field, published protocol describing how to perform quantitative colocalization analysis of confocal fluorescence microscopy images.

The protocol can be accessed here

This protocol is the most comprehensive source of practically-oriented information in the field of quantitative colocalization analysis. Researchers studying colocalization will find it absolutely indispensable.