Joanna Pylvänäinen
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jwpylvanainen.bsky.social
Joanna Pylvänäinen
@jwpylvanainen.bsky.social
1.1K followers 730 following 30 posts
Image analysis | Infrastructure | Education | Post-doctoral researcher
Posts Replies Media Videos
Reposted by Joanna Pylvänäinen
turkubioimaging.bsky.social
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️
jobs.helsinki.fi/job/Helsinki...
#jobopening
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
jobs.helsinki.fi
October 10, 2025 at 1:58 PM
Reposted by Joanna Pylvänäinen
guijacquemet.bsky.social
- A postdoc to work on cancer extravasation (4-year project).
- A postdoc help in completing Filopodia-related lab projects (2-year).
- Multiple Marie Curie postdoc positions that will open in the fall.
- We will open a 5-year position to cover my teaching (70% research and 30% teaching).
guijacquemet.bsky.social Guillaume Jacquemet @guijacquemet.bsky.social · Jun 23
Are you looking for a postdoc?
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!
July 1, 2025 at 4:46 AM
Reposted by Joanna Pylvänäinen
guijacquemet.bsky.social
Are you looking for a postdoc?
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!
June 23, 2025 at 2:29 PM
Reposted by Joanna Pylvänäinen
mycroscopy.bsky.social
Walking through streets of Helsinki. After-conference social events are the best way to finish the day. Sunny Helsinki summer night, good weather, good company, what else can one ask for? @florianjug.bsky.social @jwpylvanainen.bsky.social @turkubioimaging.bsky.social @ai4life.bsky.social
May 28, 2025 at 8:20 AM
Reposted by Joanna Pylvänäinen
strigaud.bsky.social
4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
May 15, 2025 at 12:33 PM
Reposted by Joanna Pylvänäinen
strigaud.bsky.social
Perfect way to finish the day with ☀️ and warm evening.

Thanks to the teachers and dear colleagues @jwpylvanainen.bsky.social @mambroset.bsky.social @gaellel.bsky.social @m-albert.bsky.social Carlos Garcia-Lopez & Heloise Monnet, and the students that join us !
May 15, 2025 at 12:37 PM
Reposted by Joanna Pylvänäinen
gaellel.bsky.social
Second day with Ilastik (@ilastik-team.bsky.social) covered by @MinhSonPhan, with @strigaud.bsky.social and @jytinevez.bsky.social as helpers. How to easily train a pixel classifier to segment focal adhesions..
May 13, 2025 at 10:21 AM
Reposted by Joanna Pylvänäinen
strigaud.bsky.social
Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social
May 13, 2025 at 7:57 AM
jwpylvanainen.bsky.social
Just arrived to Institute Pasteur in Paris for Neubias Image analysis course. Todays opening talk about the future of bioimage analysis by @florianjug.bsky.social - very cool week ahead! #neubiaspasteur2025
May 13, 2025 at 7:46 AM
Reposted by Joanna Pylvänäinen
benjulab.bsky.social
Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
May 12, 2025 at 5:25 AM
Reposted by Joanna Pylvänäinen
globias.bsky.social
Second round of hashtag#GloBIAS Free Help (previously Call4Help) is happening in May. You can register for the sessions on our webpage: www.globias.org/activities/g...
Registration deadline is 7. May 2025.
April 28, 2025 at 8:22 AM
Reposted by Joanna Pylvänäinen
bethcimini.bsky.social
If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis
Open Source Bioimage Analysis Training Survey
We are attempting for a publication to estimate the number of biologists who have attended a tutorial or training course in open source bioimage analysis (especially user friendly tools, but anything ...
forms.gle
April 8, 2025 at 2:32 PM
Reposted by Joanna Pylvänäinen
jcellsci.bsky.social
Joanna Pylvänäinen @jwpylvanainen.bsky.social Hanna Grobe and Guillaume Jacquemet @guijacquemet.bsky.social present their practical guidelines for data exploration in quantitative cell biology.
journals.biologists.com/jcs/article/...
#OpenAccess
Here, we show data exploration and visualization for an experiment comparing the number of filopodia in control cells with that in cells treated with siRNA targeting TLNRD1. (A) HUVECs expressing Lifeact–RFP under control or experimental conditions. Cells were fixed, stained with DAPI and imaged using spinning disk confocal microscopy. Representative maximal intensity projections of fields of view are shown. Scale bar: 20 µm. Images were acquired as part of a previously published study (Ball et al., 2024). (B) Schematic of the wide data format, where data relating to the number of filopodia counted in each condition are stored across columns, making data more challenging to manipulate for downstream analyses. (C) Schematic of the tidy data format, where each variable (e.g. condition, filopodia count, repeat) is stored in a single column, and each observation occupies a row. This organization enables flexible data wrangling, statistical analysis and direct input into visualization tools such as box plots and heatmaps. (D) The number of filopodia per GFP-positive cell as shown in A was manually quantified across all conditions (four biological repeats, >60 fields of view per condition). Results are presented as box plots, where horizontal lines mark the median, boxes represent the interquartile range, and vertical whiskers extend to data points within 1.5× the interquartile range above and below the third and first quartiles, respectively. Dot plots showing each biological replicate uniquely color-coded are also presented as part of a SuperPlot (Lord et al., 2020) to visualize variability in the data. Importantly, the tidy data format was required to make this plot. (E) Pairwise condition comparisons using heatmaps. Three mirrored heatmaps, one displaying the effect size (Cohen's d values) and two displaying the statistical significance (P-values from randomization tests with and without Bonferroni correction). The plots in D and E were generated using Plot-Stats.
April 14, 2025 at 2:01 PM
Reposted by Joanna Pylvänäinen
bethcimini.bsky.social
Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)
Ask Erin, Dear Beth
On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...
www.youtube.com
April 7, 2025 at 10:11 PM
jwpylvanainen.bsky.social
We wrote an opinion with simple, practical advice for building data exploration workflows in quantitative cell biology with @guijacquemet.bsky.social and @hanna09.bsky.social . I hope you find it useful!
April 8, 2025 at 5:26 AM
Reposted by Joanna Pylvänäinen
lacarlson.bsky.social
Repost appreciated:

Open #PhDposition in structural virology in my group! Join us in Umeå, 🇸🇪 to uncover how arboviruses remodel the cellular interior. In situ #cryoET combined with #virology, #cellbiology, and #biophysics.

Deadline 4 May. More info: www.carlsonlab.se/join/
April 4, 2025 at 8:06 AM
jwpylvanainen.bsky.social
Jamie Hyneman's lecture on creative problem solving & climate innovation was packed, so we found a cozy spot in the streaming room to watch live with @ivanhcenalmor. @aboakademi.bsky.social
April 1, 2025 at 6:58 AM
Reposted by Joanna Pylvänäinen
jcellsci.bsky.social
In their Essay, @jwpylvanainen.bsky.social, @guijacquemet.bsky.social and @lankylaste.bsky.social outline their practical recommendation for developing image analysis software for life science applications.
journals.biologists.com/jcs/article/...
Schematic of recommendations for user-friendly software development. The process of creating user-friendly software is divided into three phases, which contribute to a streamlined development process, enhancing usability and accessibility. The identified phases include: (1) software development, focused on identifying the problem and assessing the landscape, prior to defining software requirements; (2) user-friendliness evaluation to ensure ease of installation, use and maintenance; and (3) knowledge dissemination, centred on adequate documentation, distribution of the software and adoption of the FAIR (Findable, Accessible, Interoperable, Reproducible) principles.
March 20, 2025 at 10:36 AM
Reposted by Joanna Pylvänäinen
david-j-barry.bsky.social
Excellent set of guidelines for anyone developing software for life scientists, from @jwpylvanainen.bsky.social, @lankylaste.bsky.social and @guijacquemet.bsky.social

journals.biologists.com/jcs/article/...
Practical recommendations for developing software for life science applications
ABSTRACT. Developing user-friendly image analysis software is essential for advancing biological and life science research. However, the interdisciplinary gap between software developers and life scie...
journals.biologists.com
March 19, 2025 at 3:56 PM
Reposted by Joanna Pylvänäinen
guijacquemet.bsky.social
Awesome to have @henriqueslab.bsky.social join us as a visiting professor!!!
March 17, 2025 at 10:06 AM
Reposted by Joanna Pylvänäinen
guijacquemet.bsky.social
Check this one out! This is a great read (I am bias).

But Joanna and Stefania did an amazing job putting the article together.
March 17, 2025 at 10:08 AM
Reposted by Joanna Pylvänäinen
lankylaste.bsky.social
And it’s out! Thanks to @bethcimini.bsky.social and all the participants in the @biologists.bsky.social “Effectively Communicating BioImage Analysis” workshop last year for the fruitful discussions that started the idea behind this paper. Get reading and let us know what you think!
March 17, 2025 at 10:16 AM
jwpylvanainen.bsky.social
Fresh from the press! @lankylaste.bsky.social, @guijacquemet.bsky.social and I put together a practical guide on how to develop software for life science applications.
Practical recommendations for developing software for life science applications
ABSTRACT. Developing user-friendly image analysis software is essential for advancing biological and life science research. However, the interdisciplinary gap between software developers and life scie...
doi.org
March 17, 2025 at 9:44 AM
jwpylvanainen.bsky.social
Yet another throwback to my thesis work—digging into year-old data. For once, past me did future me a favor: everything nicely documented in one place! 💪🏻
February 5, 2025 at 12:52 PM