New Issue: June 1

 

Papers published in the new issue of the JCB, released today  highlight interesting new ways to view and interact with data using the JCB DataViewer.  All three data sets mentioned below can be found in the “Featured Images” section on the JCB DataViewer home page.

 

If you are unfamiliar with the JCB DataViewer and want to have a look around, a brief guide is available here.  The DataViewer is optimized to work in Firefox, Internet Explorer 7, and Safari, so if you’re having trouble loading or viewing images, try changing your browser.

 

In our cover story, there’s more to the data than meets the eye.  Yeung and colleagues in Sergio Grinstein’s lab (Hospital for Sick Children, Toronto, Canada) designed probes to detect changes in the lipid environment during phagocytosis (also covered in more detail in this issue’s In Focus).  Accumulation of multiple different probes at the site of engulfment is shown in Figure 1  in the paper (see right).  By opening the images in the DataViewer, the user can see other cells in the field (either expressing the probe or not) by turning on the phase-contrast channel, and can look at the GFP or the mRFP channels either individually or together.  If you want to see them all at once, try the split channel feature (located at the top of the left panel tool box).  This is one example of how access to original microscopy data can give the reader more information than ever possible before.

 

Have you ever taken a squint at a small histology figure panel in print or online and wished you could have a really good look at it?  As the video below shows, Nowak et al. (Centre for Medical Research, University of Western Australia) have found that cardiac isoforms of actin ectopically expressed in skeletal muscle can functionally compensate for loss of the endogenous muscle actin isoform in mice.  For a close look at the histology and EM micrographs, open Figure 3 in the DataViewer and use your mouse to zoom in – you can nearly see individual cells.  More information about the study is also featured in our latest addition of biobytes. Even the BBC picked up on this story!

 

Finally, if you’ve ever looked at that one perfect cell pictured in a figure and wondered just how “representative” it really is, click open the data from Dupin, Camand, and Etienne-Manneville.  The team forced interactions between cells using micropatterned substrates and studied the effects of cell-cell contacts on nuclear positioning and cell polarity.  Image sets used to generate numerical data for statistical analysis included with the manuscript, amounting to hundreds of images, were uploaded to the JCB DataViewer.  You can either scroll through the library of images in the minimal data viewer or open up each one separately to view cadherin, centrosome, and nuclear positioning in more detail.

The JCB DataViewer allows authors to provide their readers with full access to their original image files, including multi-dimensional microscopy data.  It’s not only common practice, but sometimes practical to show a single strip of a Western Blot as part of a figure, but our DataViewer can also be used to host original scans full-sized gels and blots.  The reader can then also inspect and interact with the data in new ways. Because the JCB DataViewer is the first software of its kind for an academic research journal, the JCB is glad to work with authors to make sure data is presented correctly.  Click here for more information about currently supported file formats. It will be exciting to watch the cache of data grow in the future, and we look forward to hearing feedback from our readers about how the DataViewer is used when reading JCB papers (use the button below to comment).