Colorblind II: Microscopy images and colour blindness – quantixed
quantixed.org
July 21, 2026 at 3:16 PM
An idea for a workshop that you can run (or take yourself!) to teach "R for cell biologists". 🧪
quantixed.org/2025/01/20/g...
quantixed.org/2025/01/20/g...
Get Better: R for cell biologists – quantixed
quantixed.org
January 20, 2025 at 2:49 PM
An idea for a workshop that you can run (or take yourself!) to teach "R for cell biologists". 🧪
quantixed.org/2025/01/20/g...
quantixed.org/2025/01/20/g...
Thank you @ucdlibrary.bsky.social for sourcing this fantastice read by @steveroyle.bsky.social for me. Highly recommended for anyone interested in learning more about #cellbiology #biologicalimaging #imageanalysis #datavis also more people should read the #quantixed blog.
January 18, 2026 at 6:24 PM
Thank you @ucdlibrary.bsky.social for sourcing this fantastice read by @steveroyle.bsky.social for me. Highly recommended for anyone interested in learning more about #cellbiology #biologicalimaging #imageanalysis #datavis also more people should read the #quantixed blog.
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Adventures in Code VII: getting started with napari – quantixed
quantixed.org
November 4, 2025 at 10:00 AM
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
IDEA: "Where are they now?" but for big splash papers published in the 2000s.
quantixed.org/2025/09/18/w...
quantixed.org/2025/09/18/w...
Where are they now? – quantixed
quantixed.org
September 18, 2025 at 9:26 AM
IDEA: "Where are they now?" but for big splash papers published in the 2000s.
quantixed.org/2025/09/18/w...
quantixed.org/2025/09/18/w...
Fascinating post from @steveroyle.bsky.social on his "academic software stack". Really useful survey of software tools, databases, calendars, note taking apps, etc. a savvy lab is using. Essential reading for new PIs quantixed.org/2025/04/29/s...
Stacked Up: my academic software stack – quantixed
quantixed.org
April 30, 2025 at 1:13 PM
Fascinating post from @steveroyle.bsky.social on his "academic software stack". Really useful survey of software tools, databases, calendars, note taking apps, etc. a savvy lab is using. Essential reading for new PIs quantixed.org/2025/04/29/s...
In this post I collated my "academic software stack".
Tried-and-tested, mostly FOSS, and geared towards Mac. For anyone that's looking for software for scientific research. 🧪
quantixed.org/2025/04/29/s...
Tried-and-tested, mostly FOSS, and geared towards Mac. For anyone that's looking for software for scientific research. 🧪
quantixed.org/2025/04/29/s...
Stacked Up: my academic software stack – quantixed
quantixed.org
April 30, 2025 at 11:36 AM
In this post I collated my "academic software stack".
Tried-and-tested, mostly FOSS, and geared towards Mac. For anyone that's looking for software for scientific research. 🧪
quantixed.org/2025/04/29/s...
Tried-and-tested, mostly FOSS, and geared towards Mac. For anyone that's looking for software for scientific research. 🧪
quantixed.org/2025/04/29/s...
oops previous link was broken: github.com/quantixed/p0...
GitHub - quantixed/p064p037: Code and data for manuscript p064p037
Code and data for manuscript p064p037. Contribute to quantixed/p064p037 development by creating an account on GitHub.
github.com
April 16, 2025 at 11:31 PM
oops previous link was broken: github.com/quantixed/p0...
ICYMI: a quick calculation of transmembrane domain-containing proteins in a proteome.
If you need to use this info: the code is in the post, or you can cite it since all quantixed posts have their own DOI courtesy of Rogue Scholar. doi.org/10.59350/0ah...
If you need to use this info: the code is in the post, or you can cite it since all quantixed posts have their own DOI courtesy of Rogue Scholar. doi.org/10.59350/0ah...
April 17, 2026 at 8:55 AM
ICYMI: a quick calculation of transmembrane domain-containing proteins in a proteome.
If you need to use this info: the code is in the post, or you can cite it since all quantixed posts have their own DOI courtesy of Rogue Scholar. doi.org/10.59350/0ah...
If you need to use this info: the code is in the post, or you can cite it since all quantixed posts have their own DOI courtesy of Rogue Scholar. doi.org/10.59350/0ah...
For followers who are into running and/or #RStats
It's marathon season. I crunched the numbers on the 2025 NY Marathon to work out how to optimally pace a marathon. There's a general rule that works if you're going for sub-2:20 or trying to make it round in 6 hours.
quantixed.org/2026/04/06/m...
It's marathon season. I crunched the numbers on the 2025 NY Marathon to work out how to optimally pace a marathon. There's a general rule that works if you're going for sub-2:20 or trying to make it round in 6 hours.
quantixed.org/2026/04/06/m...
Marathon Man: how to pace a marathon – quantixed
quantixed.org
April 6, 2026 at 1:49 PM
For followers who are into running and/or #RStats
It's marathon season. I crunched the numbers on the 2025 NY Marathon to work out how to optimally pace a marathon. There's a general rule that works if you're going for sub-2:20 or trying to make it round in 6 hours.
quantixed.org/2026/04/06/m...
It's marathon season. I crunched the numbers on the 2025 NY Marathon to work out how to optimally pace a marathon. There's a general rule that works if you're going for sub-2:20 or trying to make it round in 6 hours.
quantixed.org/2026/04/06/m...
I had to recreate a FACS plot in R, for *reasons*. It was not obvious (to me) how to make a line and fill histogram, so here's a quick post showing how to do it.
quantixed.org/2025/06/05/l...
quantixed.org/2025/06/05/l...
Let It Flow: recreating a FACS plot with ggplot – quantixed
quantixed.org
June 5, 2025 at 12:18 PM
I had to recreate a FACS plot in R, for *reasons*. It was not obvious (to me) how to make a line and fill histogram, so here's a quick post showing how to do it.
quantixed.org/2025/06/05/l...
quantixed.org/2025/06/05/l...
Materials are here: github.com/quantixed/r-...
GitHub - quantixed/r-for-cell-biologists: Teaching "R for cell biologists", not teaching R to cell biologists!
Teaching "R for cell biologists", not teaching R to cell biologists! - quantixed/r-for-cell-biologists
github.com
January 20, 2025 at 2:53 PM
Materials are here: github.com/quantixed/r-...
Still posting about R coding like LLMs haven't happened...
Loading multiple csv files into a single data frame - "R for Cell Biologists"
quantixed.org/2026/03/09/g...
Loading multiple csv files into a single data frame - "R for Cell Biologists"
quantixed.org/2026/03/09/g...
Get Better: loading multiple csv files in R – quantixed
quantixed.org
March 9, 2026 at 3:34 PM
Still posting about R coding like LLMs haven't happened...
Loading multiple csv files into a single data frame - "R for Cell Biologists"
quantixed.org/2026/03/09/g...
Loading multiple csv files into a single data frame - "R for Cell Biologists"
quantixed.org/2026/03/09/g...
Remember the Frontiers AI rat penis incident? I wondered how that affected submissions and (sorry to sound clickbait-y) the answer surprised me...
quantixed.org/2026/07/23/n...
quantixed.org/2026/07/23/n...
New Frontier – quantixed
quantixed.org
July 23, 2026 at 10:52 AM
Remember the Frontiers AI rat penis incident? I wondered how that affected submissions and (sorry to sound clickbait-y) the answer surprised me...
quantixed.org/2026/07/23/n...
quantixed.org/2026/07/23/n...
I put an ode to the Golgi into a Fiji macro I wrote and it made it into the Github repo associated with my paper 👌 Those who seek it shall find this Easter egg 🐣 on: github.com/quantixed/p0... (code snippet in the next post) @steveroyle.bsky.social
github.com
April 16, 2025 at 11:29 PM
I put an ode to the Golgi into a Fiji macro I wrote and it made it into the Github repo associated with my paper 👌 Those who seek it shall find this Easter egg 🐣 on: github.com/quantixed/p0... (code snippet in the next post) @steveroyle.bsky.social
21. Did you know there's an best time to post a preprint?
It isn't at the time of journal submission, as most do. It's ~1 month prior to journal submission. This allows you to get feedback & rack up views/metrics before submitting.
Data @steveroyle.bsky.social: buff.ly/49if305
#PreprintAdvent
It isn't at the time of journal submission, as most do. It's ~1 month prior to journal submission. This allows you to get feedback & rack up views/metrics before submitting.
Data @steveroyle.bsky.social: buff.ly/49if305
#PreprintAdvent
Exploding, Impacting: looking at bioRxiv preprint view dynamics with R – quantixed
One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab.
buff.ly
December 21, 2024 at 1:00 PM
21. Did you know there's an best time to post a preprint?
It isn't at the time of journal submission, as most do. It's ~1 month prior to journal submission. This allows you to get feedback & rack up views/metrics before submitting.
Data @steveroyle.bsky.social: buff.ly/49if305
#PreprintAdvent
It isn't at the time of journal submission, as most do. It's ~1 month prior to journal submission. This allows you to get feedback & rack up views/metrics before submitting.
Data @steveroyle.bsky.social: buff.ly/49if305
#PreprintAdvent
What stage are you at? Writing only or still working in the lab?
I wrote some advice here:
quantixed.org/2021/07/02/r...
I wrote some advice here:
quantixed.org/2021/07/02/r...
Rule of Three: advice on writing a PhD thesis – quantixed
quantixed.org
April 22, 2026 at 11:45 AM
What stage are you at? Writing only or still working in the lab?
I wrote some advice here:
quantixed.org/2021/07/02/r...
I wrote some advice here:
quantixed.org/2021/07/02/r...
Anti-streaming with FOMO over "wrapped"? No problem, with a bit of R code and an obsessively catalogued music collection you can generate your own stats!
Good grief, I listened to 77 days of music in the last year...
quantixed.org/2025/12/04/w...
Good grief, I listened to 77 days of music in the last year...
quantixed.org/2025/12/04/w...
What’s In The Box: Wrapped but not streamed 2025 – quantixed
quantixed.org
December 4, 2025 at 8:57 PM
Anti-streaming with FOMO over "wrapped"? No problem, with a bit of R code and an obsessively catalogued music collection you can generate your own stats!
Good grief, I listened to 77 days of music in the last year...
quantixed.org/2025/12/04/w...
Good grief, I listened to 77 days of music in the last year...
quantixed.org/2025/12/04/w...
I wrote simplified guide to move from Twitter/X to Mastodon.
If you find bluesky a bit meh, or if you want to try the OG federated social network (or give it another chance), you might find it useful.
quantixed.org/2024/08/14/e...
If you find bluesky a bit meh, or if you want to try the OG federated social network (or give it another chance), you might find it useful.
quantixed.org/2024/08/14/e...
Exodus: moving to Mastodon – quantixed
quantixed.org
August 15, 2024 at 8:12 AM
I wrote simplified guide to move from Twitter/X to Mastodon.
If you find bluesky a bit meh, or if you want to try the OG federated social network (or give it another chance), you might find it useful.
quantixed.org/2024/08/14/e...
If you find bluesky a bit meh, or if you want to try the OG federated social network (or give it another chance), you might find it useful.
quantixed.org/2024/08/14/e...
Would be great to have an option for "I've seen this and am happy not to see it again".
Today it's Freud on cocaine. Tomorrow it'll be something else. Amusing first time, really not by the 10th time.
Other ideas to improve feeds. Warning: contains wishful thinking.
quantixed.org/2025/01/24/n...
Today it's Freud on cocaine. Tomorrow it'll be something else. Amusing first time, really not by the 10th time.
Other ideas to improve feeds. Warning: contains wishful thinking.
quantixed.org/2025/01/24/n...
Not What You Want: improving a science social media feed – quantixed
quantixed.org
May 1, 2026 at 9:20 AM
Would be great to have an option for "I've seen this and am happy not to see it again".
Today it's Freud on cocaine. Tomorrow it'll be something else. Amusing first time, really not by the 10th time.
Other ideas to improve feeds. Warning: contains wishful thinking.
quantixed.org/2025/01/24/n...
Today it's Freud on cocaine. Tomorrow it'll be something else. Amusing first time, really not by the 10th time.
Other ideas to improve feeds. Warning: contains wishful thinking.
quantixed.org/2025/01/24/n...
So papers that are cool but also open doors to future study are ideal! Do you know one? It can be your own, I don't mind!
Last year's selection: quantixed.org/2024/01/08/p...
2/2
Last year's selection: quantixed.org/2024/01/08/p...
2/2
Papers for MD9A8 – 2024 edition – quantixed
quantixed.org
December 3, 2024 at 2:56 PM
So papers that are cool but also open doors to future study are ideal! Do you know one? It can be your own, I don't mind!
Last year's selection: quantixed.org/2024/01/08/p...
2/2
Last year's selection: quantixed.org/2024/01/08/p...
2/2
VolcanoPlotR: a new package for visualising proteomic data in R.
Explainer: quantixed.org/2026/07/15/e...
Code: github.com/quantixed/Vo...
Docs: quantixed.github.io/VolcanoPlotR/
Explainer: quantixed.org/2026/07/15/e...
Code: github.com/quantixed/Vo...
Docs: quantixed.github.io/VolcanoPlotR/
July 15, 2026 at 9:58 AM
VolcanoPlotR: a new package for visualising proteomic data in R.
Explainer: quantixed.org/2026/07/15/e...
Code: github.com/quantixed/Vo...
Docs: quantixed.github.io/VolcanoPlotR/
Explainer: quantixed.org/2026/07/15/e...
Code: github.com/quantixed/Vo...
Docs: quantixed.github.io/VolcanoPlotR/
I wrote something about why giving negative feedback to your colleagues can be a bit like slaying vampires in The Lost Boys, or something like that.
quantixed.org/2025/04/23/f...
quantixed.org/2025/04/23/f...
Feedback Deficiency: the tricky art of effective peer feedback – quantixed
quantixed.org
April 23, 2025 at 2:58 PM
I wrote something about why giving negative feedback to your colleagues can be a bit like slaying vampires in The Lost Boys, or something like that.
quantixed.org/2025/04/23/f...
quantixed.org/2025/04/23/f...
For any PB-chasers interested in using data science to pick the best Marathon event. #RStats #running
quantixed.org/2025/11/17/c...
quantixed.org/2025/11/17/c...
Choose Your Fighter: data-driven selection of the best marathon – quantixed
quantixed.org
November 18, 2025 at 1:33 PM
For any PB-chasers interested in using data science to pick the best Marathon event. #RStats #running
quantixed.org/2025/11/17/c...
quantixed.org/2025/11/17/c...
Some simple tips on making sensible-sized but high resolution movie files from microscopy data
quantixed.org/2024/03/19/m...
quantixed.org/2024/03/19/m...
Monster Movie: making movie files from microscopy data – quantixed
quantixed.org
March 21, 2024 at 8:08 AM
Some simple tips on making sensible-sized but high resolution movie files from microscopy data
quantixed.org/2024/03/19/m...
quantixed.org/2024/03/19/m...