Archive for the ‘Science’ category

ITK 3.2 released!

March 14, 2007

The new release of the Insight Toolkit (ITK) (an open source toolkit for image processing, registration, and segmentation) is available now!

From their mailing list, we have that:


We are pleased to announce the release of ITK 3.2.

You can download this release from the Download page:


or through CVS by using the tag :



The manifesto of changes in this release can be found

in the following Wiki page:




Perl Monks, Granular Computing, and World Forum on Free Knowledge

October 1, 2006

Some days ago, I attained level 3 (Acolyte) in the Perl Monks. It is nice to see how my opinions are getting good reviews 🙂 . These days, I am working on a Granular Computing tutorial for the Perl Monks community. I plan to divide it into two posts:

  1. General Introduction: from information granules to granular computing; applications: image processing, data mining, signals processing, etc.; common frameworks for Granular Computing: Interval Analysis, Fuzzy Sets, Rough Sets; and finding information granules in a Fuzzy Sets framework.

  2. Plan for a Granular Computing Module: here I present what modules are needed in Perl to write a Granular Computing Module. My idea is that we should create several (small?) modules and combine them to create the Granular Computing module. For instance, we could have a Fuzzy Sets Module (there are already some modules in CPAN related to Fuzzy Sets, so our task would be to chose one and improve it), a Rough Sets Module, an Interval Analysis Module, and a Clustering Module (I already wrote a Fuzzy C-Means script, I certainly would be happy writing all the scripts needed in this area). Our Granular Computing Module would call on these modules and add some additional functionalities. The advantage of doing it this way is that if someone is interested only on an individual module (Fuzzy Sets, Interval Analysis, etc.) that person would not need to use the whole Granular Computing Module. Moreover, I expect it to be easier to maintain smaller modules. The only problem I see with this idea is related to dependences. In any case, I guess that I will be writing a lot of Perl code this coming year 😉

The last point on this post is related to the 4th World Forum on Free Knowledge. This Forum will take place in Maturin, Venezuela from October 17 to October 21, 2006. In the Forum, I will be giving a talk titled: Open Science: Utopia or Reality? In this talk, I describes what is needed to have a truly open science, muse on whether Open Science is attainable, and present some guidelines to help us make it a reality. In the Forum, I will also give a tutorial on Image Analysis using Free and Open Source Software. The tutorial focus on my research in using Granular Computing for image analysis. I will describe my experience with the ITK and the Perl’s AI::FuzzyInference module in my quest for finding a way to help content experts in analyzing images. I will post more on that later.



My first steps with Perl!

September 22, 2006

By the end of OSCON, Alejandro had convinced me that I should try Perl. So I decide to buy a couple of books to get started. If you are curious, I bought Learning Perl (the Llama book) and Mastering Algorithms with Perl. By the end of July, I started learning. Maybe it is just me, but I found Perl to be an easy to learn language (I did a lot of assembly and C programming before). On August, I made a decision: I would code an important portion of my Research work in Perl. That is me, very passionate some times.

To help me with this task, I bought another book (this time it was the Alpaca book –Intermediate Perl) and joined the Perl Monks. After reading a bit of the book (I have not had the time to finish it), I started to port some code that I had in MATLAB to Perl. I decided to start with one of my favorites: a Fuzzy C-Means implementation. You can see it on my Perl Monks’ scratchpad. It works! By the way, if you are a Perl’s expert and have a suggestion or two on how to improve my code, feel free to drop me a line. Remember: I have been programming in Perl for less than two months.



Nature is undertaking an Open Peer Review trial

June 29, 2006

For the next three months, Nature is conducting an open peer review trial. Authors submitting articles for peer review are given the option to participate also in a open peer review process in which their papers are open for public comments. The public comments will not have an effect on whether or not the papers are accepted in Nature. However, at the end of the trial the Editors of Nature will study the comments to assess their value.

Even though this is a great initiative, I do not think that three months is enough for this type of trials. Anyways, kudos to Nature for trying new ways to improve the traditional peer review process.

For more information:

Nature’s home page

Nature’s page on the peer review trial

FAQ’s on the trial


Back from Montreal

June 8, 2006

This trip to Montreal went much better than I expected, even tough it did not started on the right track. I tried to use the web check-in system from Air Canada and I could not figure out why it did not work. Then, I had some things to do before leaving home and I arrived late to the airport. I got there 35 minutes before my flight. I tried to use the automated check-in counter but it did not work either. After a while, a person from Air Canada told me I had to do the manual check-in. I waited in line and when I arrived to the counter there were 25 minutes before my flight and the person in the counter told me that I could not flight because I was too late (at that time I missed West Jet, their personnel always try to help you instead of making it hard for you). Well, I paid the CAD $ 150 for the change and went through security. After security I noticed that they were calling for the general boarding of the flight I was supposed to take. I waited patiently and ask one of the persons at the Air Canada counter whether the flight was full and she told me that it was not. I ask her whether I could take the flight and told her what happened to which she simply replied that it is Air Canada policy, I have to check-in at least 30 minutes before the flight or they simply do no let me flight. I guess there is only room for only one Airline like WestJet in Canada where the passengers are priority number 1.

Anyway, I arrived in Montreal and went to the Residences of the University of Montreal where I was going to stay. Everything was ok with the room. On Sunday morning, I went to the conference venue and attended several talks: the opening talk by Prof. Zadeh, the father of Fuzzy Logic, a talk by my previous supervisor, Prof. Pedrycz, a world-expert on Granular Computing, and some others. At noon I had a chance of having lunch from a couple of representatives from Decyde Inc., they are using fuzzy rules based system for automating the decision-making process in different areas.

During the afternoon, I attended a second plenary talk and I was surprised to know that my paper was selected as one of the top-five students papers. So I was invited to the banquet to receive my award (a nice certificate and a US$ 100 check). Later that afternoon, I gave my talk and it was well received. I had lots of questions and people wanted to continue commenting and discussing our approach 😉
In the evening, I went to the Ubuntu release party at the Cafe L'Utopik. I met really nice people, several employees from Canonical (the organization behind Ubuntu) and Fabian Rodriguez from FACIL (a group that promotes Free Software in Quebec). Fabian invited me to visit the FACIL headquarters and I agreed with that. Unfortunately, I had to leave early because I had to attend the banquet (remember, to get my US$ 100 cheque 😉 ).

I went to the banquet and sit with a Prof. from Regina and one from the Canadian East Coast. The dinner was great and the company was too.

After the banquet, I went back to the residence to rest and prepare for Monday. Monday morning, I went to the conference again, attended a couple of talks and then I went to meet with the Venezuelan General Consul. We talked about Free Software and what we are doing in Venezuela to promote it. The General Consul is a person really committed to help Free Software becoming part of Venezuela's reality. His radio station is the one you can see in the video Free Software: Venezuelan Chapter that I promoted some time ago. After meeting with the General Consul, I had a meeting with one of the Consuls and I had lunch with him. These guys at the Venezuelan Consulate really understand Free Software and the social implications of it.

After my meetings at the Venezuelan Consulate, I went back to the conference venue. There, I attended a couple of talks and later I went to meet with the people of FACIL. I had a wonderful time thanks to Marc Angles and Fabian Rodriguez. They did a small interview in which I explained what is happening in Venezuela with the discussions for the new Free Software Bill.

Fabian gave me a ride back to the residence around midnight.

On Tuesday morning, I came back to Edmonton. I arrived in the Afternoon. And I have been spending most of the time trying to find accommodations in Europe where we go this weekend. Wish me luck!


Going to Montreal!!!!!!!!

June 3, 2006

Today at 13h20, I will be taking a plane to Toronto and then Montreal. I will be presenting a paper at NAFIPS 2006 (NAFIPS are the initials of North American Fuzzy Information Processing Society). The paper is about a framework I developed for automatically setting the parameters in an image matching tool. But, what is image matching? Image matching is the process of aligning images to better analyse changes between the two of them. The “cool” part about my research is that it is “useful” . It is more than just a theory that a PhD student developed, it is something you can use in clinical applications. I will start writing about my research when I come back.

By the way, because I will be in Montreal, I will be able to attend an Ubuntu Dapper release party. Here are the particulars 😉

  • Why: We released Ubuntu 6.06!
  • Where: … ( I am not sure whether I am allowed to inform that 😉 )
  • When: Sunday, 4 June 2006 at 18:00

I hope to see many Ubuntu fans over there 😉


The Euroscience Open Forum 2006 promises to bring science to the people

May 31, 2006

Euroscience Open Forum 2006 ( ESOF2006 ) will take place in Munich, Germany from July 15th to 19th, 2006. ESOF2006 is hosted by Wissenschaft im Dialog ( WiD ), a non-profit organisation founded by the most significant research funding organisations in Germany. WiD’s purpose is to promote interaction and dialogue between science and the general public. The impressive ESOF2006’s program includes sessions such as:

  1. Bringing science to the people
  2. European science policy: gloomy forecast vs. bright horizons
  3. The European Research Council: who are the movers and shakers?
  4. What do you expect from science?
  5. Green chemistry: a tool for socio-economic development and environmental protection
  6. The story tellers of science: architects of culture?
  7. Open Access: threat or blessing?
  8. Standing on the shoulders of giants: mentor-inspired genius
  9. Quality science journalism: is a new style needed?

The full programme is available at