A collection of works I did outside this blog!
Outreach and teaching
- Since 2024, I became an official The Carpentries instructor. And since 2025, I became an official maintainer of the image processing with Python curriculum.
- Together with GloBIAS, we are working on redesigning the curriculum to make it more focused on bioimage analysis. Find the WIP repository here
- I have designed and taught (with colleagues) a one-afternoon Jupyter introductory journey for image anlaysisi called PyxelPerfect. You can find all the material here.
- I have organized and created material for a Python beginner-friendly course. All the material can be found in this Gitlab repo. The slides are available here.
- I have co-organized and taught a Git and Python for bioimage analysis course. The material is availble at this Gitlab repo.
Miscellaneous presentations
- A seminar on digital project files and folders control and organization using tools such as Quarto, Pandoc, LaTeX and Jupyter. Re-watch the presentation here. All the examples on which the talk is based on at available here. Slides can be found here
- A seminar on Deep Learning fundamentals and applications for bioimage analysis. Slides can be found here
- A small talk about the importance of bioimage analysis in quantitative biology. Slides can be found here
Miscellaneous articles
- MV-learn was listed in the winners of the 2024 plotnine plotting contest, with our ClockPlot invention! Find the commentary here and the code here
- I wrote a primer on image file formats and naming conventions here
- I curated and illustrated several articles for Medium together with Valeria. Here are a few examples:
- I wrote and presented an extended article on the Dos and Don’ts of data visualization, find it here
- I wrote a comparison between several Python plotting libraries, you can find the article here
- [ITA] Ho scritto una serie di articoli divulgativi, incentrati sui concetti basi di biologia cellulare per spiegare meglio e fare chiarezza su com’è fatta una cellula, quali sono i suoi funzionamenti e come questa possa diventare un tumore. Li puoi trovare qui!
Reproducibility and Version Control material
In collaboration with Valeria, we are creating teaching material on the theme of reproducibility, especially in science and academic. Check out our MV-learn project here and its GitLab group here!
- We originally taught a lecture on fundamentals of Git for version control as part of a university course, but we want the material to continue to be freely available. You can find the slides here.
- I later made a written tutorial on fundamentals of version control to make it easier for a person to follow the material independently. You can find it here.
- For a talk in the UNAL university in Colombia, we created a presentation (in Spanish) for a broader audience on the issue of reproducibility and how to address it. You can find the slides of the talk here.
- We gave a workshop to get people started with Quarto for dynamic, reproducibile and modern presentations. Check out the slides here
Scientific contributions
- We published a collaboration paper on imaging-based cell migration assays on the Biochemical Pharmacology Journal
- You can find a good summary of several analysis projects I worked on as an bioimage analyst in my professional portfolio
- I have written a personal technical guide to quantitative Förster Resonance Energy Transfer (FRET) imaging during my PhD, as a reminder and a guide for myself. It can still have some value for some other fluorescence imaging audience. You can find it here
- My PhD first author publication on improved spectrally-tunable biosensors was published here
- I published another paper during my PhD in collaboration with another group, you can find it here
“We live therefore we learn” podcast
Check out our podcast, where me and Valeria talk about our surprising experiences, deep thoughts and hidden learnings! You can find all the episodes here!