Cris’ Image Analysis Blog

theory, methods, algorithms, applications

Cris Luengo's Curriculum

Education

I have an MSc (1998) and a PhD (2004) degree in image analysis from Delft University of Technology (The Netherlands). In 2011 I received the Swedish title of Docent, which confers the right to direct PhD studies and is comparable to the French and German Habilitation.

Employment

While pursuing my PhD studies, I was employed for 1/4 of my time as a teacher at the Department of Applied Physics (later Applied Sciences) (2001–2003). I designed and taught assorted hands-on computer courses, including an introduction to image analysis using DIPimage.

After defending my PhD thesis, I joined the Life Sciences Division, Lawrence Berkeley National Laboratory (Berkeley, California, 2004–2008) as a postdoctoral fellow. There I worked with the Berkeley Drosophila Transcription Network Project developing the first 3D atlas of gene expression in the fruit fly blastoderm. I built the tools that detected all cells and quantified their expression level in 3D, two-photon scans of whole embryos.

I then became Associate Professor at the Centre for Image Analysis (Uppsala, Sweden, 2008–2015), a collaboration between Uppsala University (UU) and the Swedish University of Agricultural Sciences (SLU). My office was at the Department of Information Technology of UU, and my students came primarily from that department and the Engineering department.

From 2015 to 2022 I worked at Flagship Biosciences Inc. (Broomfield, Colorado), where I developed the tools used internally to provide quantitative, actionable data from whole slide tissue images (pathology) in a clinical setting.

I currently work at Deepcell Inc. (Menlo Park, California), which is building a cell counter and sorter that uses only cell morphology, derived from high-speed imaging, without applying any biomarker, labels or stains at all.

Software projects

I’ve been involved with the DIPlib project since starting as a PhD student at Delft University of Technology in 1999. DIPlib is an extensive library of image analysis functionality, originally written in C. I created the DIPimage toolbox for MATLAB, which soon became DIPlib’s main interface. In 2014 I started pushing to port DIPlib to C++, and make it open source. I finally started work on this myself around 2016, eventually joined by some colleagues. DIPlib 3 is now a production-quality library in C++, much easier to use than the original C library. It comes with an image viewer and C++ bindings to Bio-Formats. We also have Python bindings.

Other publicly available projects are:

  • libics, the reference library for the ICS file format.
  • dox++, a Python program to generate documentation from comments in C++ source code, similar to Doxygen but much better. I developed this to produce the DIPlib documentation.
  • mdx_math_svg, a Python-Markdown extension to render LaTeX equations as embedded SVG. This plugin is used by dox++, and on this blog.

Activities

I have been on the editorial board of Pattern Recognition Letters (Elsevier), first as Associate Editor (2011–2013), then as Area Editor (2013–2015). I was on the editorial advisory board for Mathematical Morphology - Theory and Applications (De Gruyter) since its inception in 2016, until 2021.

I have co-organized the 11th International Symposium on Mathematical Morphology (ISMM), in Uppsala, May 27–29 2013. I was the Program Chair. The proceedings to this conference were published by Springer in their LNCS series. After the conference I edited a special issue in Pattern Recognition Letters on the topics of the conference. I am on the Steering Committee for DGMM (previously DGCI and ISMM conferences).

I was Workshops, Tutorials and Contests Co-Chair for the 22nd International Conference on Pattern Recognition (ICPR, Stockholm, August 2014), and Tutorials Co-Chair for the 23rd ICPR (Cancún, Mexico, December 2016).

I am Senior Member of the IEEE, and also involved with the IEEE Signal Processing Society and the NVPHBV (Dutch Society for Pattern Recognition and Image Processing).

I speak Dutch, Spanish, English and Swedish.

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