User: How to model
User: plugin help file
User: Blender survival guide *updated
Programmer: How the skin is done
Other IJ plugins
About the author
Hire me or donate
About the author
Currently I'm enrolled at UCLA working together with Prof. Volker Hartenstein in Drosophila neurobiology. I'm working on both confocal and electron microscopical three-dimensional reconstruction of fly brain connectivity, focusing on early larvi. My postdoctoral position enables me to travel all over the world pursing research collaborations, such as this past Fall at the Max Plank Institute CBG in Dresden, where I worked with Pavel Tomancak of BGDP Expression Patterns fame.
My status today (October 2005 - January 2007)
So far so good, and so fun! I've attended the Image Conference 2006 last May in Luxembourg, the International Symposium on Flatworm Biology in Innsbruck (ISFB) last July 2006, the Neurofly meeting in Leuven, Belgium, last September, and the Blender 2006 Conference in Amsterdam.
I was hired starting June 2005 by Rodney Douglas from the Institute of Neuroinformatics at the University of Zurich / ETH to develop TrakEM2, ImageJ-based software for 2D-assembling of optical and electron microscopy images (stitching using transparencies and semiautomated methods of image recognition), their alignment in the Z axis and the posterior 3D modelling of interesting structures, using part of the A_3D_editing plugin functionality. The program aims at delivering an useful suite for broad scope 3D modelling and also an intuitive, guided interface built on top of a highly interlinked data structure for optimized data retrieval starting at any point of the process. So far so good, I'm loving the workplace!
Programming work: TrakEM2 at the Institute for Neuroinformatics, Zurich (June - September 2005)
I'm enrolled in the Genetics PhD program at the University of Barcelona. Currently I'm wrapping up my work on flatworm development into a -hopefully- readable thesis, which I'd like to defend as soon as possible. The main topic of the thesis is triclad embryogenesis.
Thesis work 2000-2005
Starting at year 2000, I have pursued multiple approaches including monoclonal antibody generation, immunohistochemical stainings, in situ hybridization and conventional histological stainings in both sectioned and whole-mount preparations, in an attempt to label Schmidtea polychroa embryo cells for the description of tissuegenesis and organogenesis with the maximum level of detail. Together with Professor Volker Hartenstein from the University of California Los Angeles, we have described the embryonic development in 8 stages (Cardona et al 2005) for a readily identification of embryos. The Hartenstein lab has been a continued source of help and suggestions, and I regard as invaluable the time I have spent there over the years.
Confocal microscopy and ImageJ have been a large part, if not the most important, in gathering and processing new data on the field. For the later I'm most grateful to Wayne Rasband and the ImageJ mailing list, in particular to Jarek Sacha (ij-ImageIO), for their continuous help and fruitful interaction.
Furthermore I have attempted to culture embryos in vivo, observing vitellocytes motile behaviour and enabling the injection of colchicine and GFP expression plasmids into the embryos.
Ultrastructural data resulted most revealing. Transmission and scanning electronic microscopy has been performed in all embryonic stages of development. Most interesting, ultrastructural analysis of vitellocytes has produced highly relevant data, soon -hopefully again- to be published.
As a side project to my thesis, I have developed several programs for 3D data manipulation and visualization, in particular the A_3D_Editing plugin for ImageJ presented in this website. The main motivation being that no other software package enabled the modelling of the very particular embryonic structures I came across, such as the highly-branched nerve cells in the early embryos (see gallery). But I got carried away and I ended up with a whole suite for 3D modelling over confocal stacks of images, which I have released under GPL.
My research training has been not only in developmental and molecular biology techniques but also in computer science, namely scripting programs and setting up workstations and servers. My last project involves setting up a render farm for Blender.
The development and updates of the A_3D_editing plugin are being done on an old (2001) Apple PowerBook running java 1.3.1 and 1.4.1 (now 1.5.0 under Ubuntu GNU/Linux), which I have to keep switching to avoid the many problems both java versions have under MacOSX 10.2.8. I have no funding for neither updating the hardware nor the software.
Hire me and/or donate
If the A_3D_editing plugin has been useful to you and you're looking forward to maintenance and improvements, please consider a donation. Any donations are welcome, for instance a macosx 10.3 installation disk or a newer PowerBook.
Please note: The email displayed in the PayPal account is different from my usual email, and it's a gmail account starting with an 's'.