Nicola Romanò @nicolaromano@qoto.org
Senior lecturer at the Zhejiang-Edinburgh Joint Institute (ZJE) and Edinburgh University.
Undergraduate Programme Coordinator, Biomedical Informatics at ZJE.
I teach #imageanalysis & #dataanalysis with #RStats & #python. I study #heterogeneity in #pituitary (and other) cells.
I'm also very interested in #reproducibility and #openscience.
Joined Oct 2022
@MCDuncanLab yeah I was a bit baffled by the stash of totes as well, although I did use to have a stash of plastic bags under the sink... However I'm fascinated by the marketing that goes around this.
@CrisLuengo right, that makes sense, thanks for clarifying!
Interesting article on "reusable" products
"An entire generation has been socialized to participate in environmentalism by way of consumerism"
https://www.theguardian.com/environment/article/2024/jul/30/reusable-tote-bags
@CrisLuengo Thanks for raising that point. I have been thinking about this and I am wondering, though, wouldn't the same reasoning work for say, Sobel? Unless you threshold the gradient magnitude you are not really extracting edges by convoluting with a Sobel kernel.
Similarly, while the LoG is not per se an edge detector, finding its zero-crossings allows you to detect edges (indeed, you can also use LoG as a blob detector by finding its extrema).
So, is it just a question of semantics (LoG as a filter used in edge detection vs LoG as an edge detector), or is there more?
I am curious, as there is definitely a lot of literature saying that LoG is an edge detector.
New Python Shiny app for my image analysis course deployed!
This will accompany the lecture on edge detection methods.
https://apps.nicolaromano.net/EdgeDetection/
Source code is here, feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Apps/EdgeDetection
Nicola Romanò
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@LianaBrooks excellent points! May I add:
Privilege comes in many shapes and sizes, it’s not all-or-nothing, so you can have various types of privilege without having every possible advantage in life. You can have struggles & suffer injustice and still have privilege in some form. You can have privilege in one area and lack of privilege in another.
"Freshening up" the material for my #biomedical #image #analysis course restarting in September.
A lot of my students will be essentially #Python novices... so here is some short Python starting/refresher material! Everything's CC-BY-4.0 so feel free to reuse!
https://github.com/nicolaromano/BIA4/tree/main/Workshops/00%20-%20Preliminary%20material
@tangming2005 Absolutely agree with this. I've recently scrapped a (fairly complex and difficult to interpret) NN pipeline for transcriptomics analysis for a much simpler XGBoost pipeline and performance is the same or higher in all cases.
Also, interpretability is much higher.
Nicola Romanò
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Looking for literature for review paper:
Is there quantitative data that beauty/aesthetics in charts help user engagement/effectiveness/memory?
Nicola Romanò
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Great new blogpost by Eiko Fried on “zombie theories” in science, research waste, and moving forward. #OpenScience #academia
https://eiko-fried.com/zombie-theories-why-so-many-false-ideas-stick-around/
Nicola Romanò
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Everybody's Free (To Write Websites)
Enbies and gentlefolk of the class of '24:
Write websites. If I could offer you only one tip for the future, coding would be it. The long term benefits of coding websites remains unproved by scientists, however the rest of my advice has a basis in the joy of the indie web community's experiences. I will dispense this advice now:
Nicola Romanò
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I can't believe that in 2024 we still have to explain so bluntly that "Academic journals are a lucrative scam". Yet here we are ...
Kudos to the Editorial Board of Philosophy & Public Affairs for resigning en masse and thank you to Arash Abizadeh for explaining why and what's next in the Guardian:
https://www.theguardian.com/commentisfree/article/2024/jul/16/academic-journal-publishers-universities-price-subscriptions
Nicola Romanò
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"'With the R515 driver, #NVIDIA released a set of #Linux GPU #kernel modules in May 2022 as open source with dual GPL and MIT licensing. […]
Two years on, we’ve achieved equivalent or better application performance with our open-source GPU kernel modules […]
We’re now at a point where transitioning fully to the open-source GPU kernel modules is the right move, and we’re making that change in the upcoming R560 driver release. […]'"
https://developer.nvidia.com/blog/nvidia-transitions-fully-towards-open-source-gpu-kernel-modules/
@dan and the big issue is that even when these things are called out (and I suspect a lot of times they aren't) universities tend to pretend nothing is going on and do as minimum as possible, meaning the person who has been harassed is the one who takes the worst of an already terrible situation
Nicola Romanò
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Advantages of submitting first to the @biorxivpreprint : as an editor, I can share the entire paper with prospective reviewers to entice them to review it.
Let me tell you: this is a massive deal. Finding reviewers willing to commit to submit a review "soonish" (less than 2 months) is becoming tough.
Nicola Romanò
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I'm thinking about the FAIR (findable, accessible, interoperable, and reusable) principles of data. Much of our data is Western blots. Amongst colleagues, we were discussing how hard it would be to make it 'findable' which would require metadata schema, but I'm reconsidering it now.
I found a German paper from 2015 that has not really been cited and is more theory than practice. I wonder if anyone is actively working on this?
I'd be happy to participate.
@Mehrad That's odd, I never encountered any problems with Fedora (I'm currently running 39, is it possible that 40 is so much worse?)
@cyrilpedia you got to appreciate this little gem . I'm assuming an aptronym, but could be a zombie...
Nicola Romanò
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I've been made redundant from my job, effective tomorrow.
So... if you know anyone who's in need of a bioinformatician to work remotely on small bioinformatics projects, please let me know.
Nicola Romanò
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'Correlation is not causation: this simple and uncontroversial statement has far-reaching implications. Defining and applying causality in biomedical research has posed significant challenges to the scientific community. In this perspective, we attempt to connect the partly disparate fields of systems biology, causal reasoning, and machine learning to inform future approaches in the field of systems biology and molecular medicine'
https://www.embopress.org/doi/full/10.1038/s44320-024-00041-w
Senior lecturer at the Zhejiang-Edinburgh Joint Institute (ZJE) and Edinburgh University.
Undergraduate Programme Coordinator, Biomedical Informatics at ZJE.
I teach #imageanalysis & #dataanalysis with #RStats & #python. I study #heterogeneity in #pituitary (and other) cells.
I'm also very interested in #reproducibility and #openscience.
Joined Oct 2022
