ggplot2 2.0.0 has been released


Package photobiologygg is NOT compatible with the just released new version of package ggplot2. I knew this was coming but I will still need some days before getting my own package updated. I had used unexported functions, and of course this was dangerous. The good news is that the improvements in ggplot will allow me to implement the same functionality without need for the “illegal tricks” I had earlier used.

Sorry about my delay with this! If you use photobiologygg please, wait a few days before updating ggplot2.

A preprint archive for Biology

bioRxiv logoArXiv ( has been available for some years for storing preprints of articles on Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics.

A newer development is BioRxiv ( for preprints related to Biology. This archive has a section dedicated for Plant Biology. I found some interesting preprints in it.

It will hopefully become an important resource for our research community.

Digital imaging: stretching the limits


In coming months I will write a series of posts with brief presentations of imaging methods that are nowadays accessible and very useful for research. In many cases they are of help also for other types of documentary photography and for artistic photography. Some of these methods have been around for some time, but their use has become easier as cameras and computers, and their software have evolved. The posts will be brief but will contain links and references to help those who want to explore them in more depth. I will show examples of both software and equipment. In most cases I will include example pictures produced by myself.

I will in the first few posts describe methods that involve merging of separate shots. These methods can be used with any digital camera with manual controls and/or specific automated functions. Some modern cameras can even do the image merging almost in real time. Most of the methods can be also used with digital images obtained with a microscope.

Methods based on image merging

  • HDR: high dynamic range, the merging of images obtained using different exposure values into a single image representing a wider range of luminosities within the curve extending from black to white.
  • Focus stacking: the merging of images obtained with the focus point slightly shifted into a single image with more depth of field. In other words with a wider distance between the nearest and farthest point in sharp focus.
  • Panorama: merging of partially overlapping images into an image with more pixels and a larger subject area.
  • Enhanced resolution: merging of images displaced by less than the size of a single pixel to obtain images at a higher resolution than the sensor’s pixel resolution.
  • Object removal: removal of moving objects by merging images obtained when the moving object(s) covered different areas of a background of interest.

Methods requiring special cameras or modified normal cameras will  be described next.

Methods extending the wavelength range or wavelength resolution

  • Thermal imaging: the pixel values describe temperatures, which are derived from emitted infra-red sensed through and especial detector and lens.
  • Digital photographs at wavelengths outside those visible to us: imaging based on ultraviolet or infrared radiation.
  • Hyperspectral imaging: normal digital images have three components: red, green and blue (RGB). In spectral images each pixel is represented by spectral data of much higher wavelength resolution. Hyperspectral images are spectral images in which the spectral range extends outside the range of wavelengths visible to humans.

Methods involving extending or contracting time

  • Time lapse: merging of static images into a video with accelerated time
  • High speed photography: imaging of objects moving at very high speed for reproduction at a slower frame rate.

Limits to image manipulation

  • How much can one edit a documentary image without misrepresenting the object being documented? This is a controversial question both for images used in scientific and news reporting.
  • Image edition and reproducibility. Destructive and non-destructive methods of image manipulation. Loss-less and lossy image compression.

The reason behind this series of posts is that these methods are in use, or will be soon in use in my research group. I would have anyway to write this texts for those working with me, so why not do this is in open?