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 ¼ 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 the DIPimage toolbox for MATLAB.
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 at cellular level. I built the tools that detected all cells and quantified their expression level from 3D, two-photon scans of whole embryos. I also established the imaging protocol, helped design the database, and analyzed the gene expression patterns.
I then became Associate Professor at the Centre for Image Analysis (Uppsala, Sweden, 2008–2015), at the time 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. During this time I had 6 PhD students successfully defend their thesis, and advised a long list of MSc and undergraduate students. I collaborated with tons of researchers from across both universities, learning a lot about pathology, ophthalmology, material sciences, foresty, bees, …
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. This involved segmenting cells and muscle fibers, unmixing stains, aligning sections, and a whole lot of other interesting stuff.
I currently work at Deepcell Inc. (Menlo Park, California), where we designed and built a single-cell imaging and sorting device that uses only cell morphology, derived from high-speed imaging, without applying any biomarker, labels or stains at all. The instrument uses a foundation model for cell morphology that we created, which allows interactive exploration of the cells in a sample through an intuitive interface. My code processes hundreds of frames a second, detecting, segmenting and quantifying cells as they flow through the microscope. I also designed the logic behind the innovative autofocus system, and wrote algorithms to align the microfluidics chip to the instrument before each run.
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 took over from SCIL-Image as 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 interactive image viewer, C++ bindings to Bio-Formats to import images from just about any image file format, and 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.
Academic Activities
[I stopped doing most of these things when I left academia; here’s a summary of the more international activities.]
I was 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 member of the IEEE Signal Processing Society and the NVPHBV (Dutch Society for Pattern Recognition and Image Processing). I served on the IEEE Signal Processing Society’s Bio Imaging and Signal Processing Technical Committee.
Other
I speak Dutch, Spanish, English and Swedish.
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