OPEN SCIENCE

We are strong advocates of open access publications and open source as a model to promote a universal access to our developed tools, and share them with the scientific community through availability in an open repository. Please, surf around and if you are interested in using any of our tools, do not hesitate and do so. The only think we ask you is to quote us.

You can find below our initiatives in Public Dissemination of Science too.

 

DEVELOPED TOOLS

Image processing tools

  • Live imaging data – and particularly SPIM data – can be very large and difficult to process. We have found that rather than working with a single large file, it is convenient to work with sets of files. Let’s say for a movie with 400 time steps and two channels, you would create a single file with a unique name for each channel and time point. You can then iterate over these files, concatenate all of them or a subset (x, y, z), process them in batch, save them etc. This enables you to: i) work with your data more efficiently by developing your processing pipeline on a reduced representative set of your data, for example every 10th time point or just the region of interest; and ii) save space by saving a processing pipeline, that you can reproduce any time, rather than a lot of heavy processed data.

 

  • We have created a small ImageJ script that allow you to do the following:

    1. Create a set of files with specific naming from your large microscopy file.

    2. Register your movie in a semiautomated manner (see movie N : CB_18H) you choose a fixpoint that you would like to be always in the same location (x, y, z) in your destination files. You are guided through the frames of the movie and click on that point for each frame. The script then generates the image files with these transformations. Apart from compensating for morphogenetic movements, this operation will likely allow for cropping the data in x, y, z and can save you significant amounts of disk space.

    3. Compensate for fluorescence bleaching or lighting up of transgenic lines.

    4. Generate movies of the process you want to show by extracting only the z plane of interest or a small volume for a maximum intensity projection (see movie M).

    5. Iterate over your files and do any wished processing.

We are currently improving these tools  to make them more generic and user friendly. Soon you will find them on this page.

If you need such functionality please contact us and we will be happy to share these tools with you (e-mail: sylvia.dyballa@upf.edu)

 

PUBLIC DISSEMINATION OF SCIENCE (last 5 years)

The Universitat Pompeu Fabra strongly believes that public universities have an obligation to inform the public of their work, and to establish an open dialogue with society with regards to findings that may have a strong impact on health and society. Members of Pujades lab are highly committed to the Public Dissemination of Science and contribute to the dissemination of their findings to a larger non-specialized public.

  • STEAM Conference 2018, participant in the Round Table STEAM and Gender;

  • La Central 2018, coordinator of the course Un tastet de neurociències: del cervell sensorial al cervell social;

  • BCN Maker Faire 2017, chairwoman in the session: Gene Editing and Genomic Technologies: how synthetic biology will impact future society?;

  • Round Table: Què serà noticia en ciència? Master de Comunicació Científica UPF, Barcelona 2017;

  • YOMO: Youth Mobile, World Mobile Congress, Barcelona 2017;

  • Amb Filosofia C33-TV3, La natura 2017;

  • Let’s move to 4D-biology: building the embryonic inner ear!, The Node 2017

  • Interview to Cristina Pujades in EXCODRA, 2017 

  • Summer School in Molecular and Theoretical Biology, 2016 CRG-UPF

  • Centre Cívic Urgell: Building the brain: receptes i plànols per fer un cervell, 2015

  • Centre Cívic Urgell: Tastets de neurociències, 2015

  • PRBB Biojunior, 2015

  • Fira de la Recerca en Directe: Seguint el llinatge cel.lular in vivo: com podem veure la dinàmica de les cèl•lules durant el seu desenvolupament embrionari?, 2015

  • Centre Cívic Urgell: Receptes i plànols per fer un cervell, 2015

  • El problema de Gettier, La Xarxa 2014

  • Desarrollo y evolución del rombencéfalo: una història compartida, Mente y Cerebro, 2014