iiinova — where your digital self keeps evolving

Reposted by Joanna Pylvänäinen

Turku BioImaging @turkubioimaging.bsky.social · 10/10/2025

🚀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

jobs.helsinki.fi

Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging

12221

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 01/07/2025

- 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).

46559

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 23/06/2025

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 !!

07087

Reposted by Joanna Pylvänäinen

Elnaz @mycroscopy.bsky.social · 28/05/2025

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

093

Reposted by Joanna Pylvänäinen

Stéphane Rigaud @strigaud.bsky.social · 15/05/2025

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

1146

Reposted by Joanna Pylvänäinen

Stéphane Rigaud @strigaud.bsky.social · 15/05/2025

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 !

062

Reposted by Joanna Pylvänäinen

Gaëlle Letort @gaellel.bsky.social · 13/05/2025

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..

195

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 13/05/2025

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

3334

Reposted by Joanna Pylvänäinen

Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025

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...

719354

Reposted by Joanna Pylvänäinen

GloBIAS @globias.bsky.social · 28/04/2025

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.

22921

Reposted by Joanna Pylvänäinen

Journal of Cell Science @jcellsci.bsky.social · 14/04/2025

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.

172

Reposted by Joanna Pylvänäinen

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/04/2025

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)

youtube.com

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...

15630

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 08/04/2025

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!

02510

Reposted by Joanna Pylvänäinen

Lars-Anders Carlson @lacarlson.bsky.social · 04/04/2025

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/

12330

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 01/04/2025

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

191

Reposted by Joanna Pylvänäinen

Journal of Cell Science @jcellsci.bsky.social · 20/03/2025

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.

0105

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 17/03/2025

Awesome to have @henriqueslab.bsky.social join us as a visiting professor!!!

0233

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 17/03/2025

Check this one out! This is a great read (I am bias). But Joanna and Stefania did an amazing job putting the article together.

0248

Reposted by Joanna Pylvänäinen

Stefania Marcotti @lankylaste.bsky.social · 17/03/2025

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!

0111

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 05/02/2025

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! 💪🏻

040

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 04/02/2025

To publish or not to publish? And where to publish? Hopefully @guijacquemet.bsky.social can answer some of these questions in his presentation today. @aboakademi.bsky.social

150

Reposted by Joanna Pylvänäinen

Máté Varga @mvargam.eurosky.social · 31/01/2025

And with that the first ever @v4sdb.bsky.social Student Winter School came to the end. Thanks for all for coming, and you will be able to find all the course material on the website: danio-elte.github.io/2025V4SDBStu...

141

Reposted by Joanna Pylvänäinen

Jean-Yves Tinevez @jytinevez.bsky.social · 30/01/2025

We just released and uploaded a new version of *Mastodon*, the large-scale tracking and track-editing framework for large, multi-view images. Mastodon is available via Fiji, via a dedicated update site. mastodon.readthedocs.io/en/latest/do... Below is a thread that survey some of the novelties ⏬️

312744

Reposted by Joanna Pylvänäinen

Laurent Guerard @lguerard.bsky.social · 14/01/2025

2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year ! 2025.zidas.org

2025.zidas.org

ZIDAS 2025

This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.

11812

Reposted by Joanna Pylvänäinen

Petra Kompanikova @petrakompanikova.bsky.social · 30/01/2025

Great talks and hands-on sessions at @v4sdb.bsky.social's Winter School 2025 in beautiful Budapest! 🤗 Yesterday, @jekely.biologists.social.ap.brid.gy and @jwpylvanainen.bsky.social guided us through CATMAID, TrackMate, and CellTracksColab. 🧫 More imaging data analysis and programming ahead! 🧑‍💻

082

Reposted by Joanna Pylvänäinen

Máté Varga @mvargam.eurosky.social · 29/01/2025

The second day of the @v4sdb.bsky.social WinterSchool started again with @jekely.biologists.social.ap.brid.gy and some nice CATMAID-based analysis of the Platynereis connectome, followed by @jwpylvanainen.bsky.social talking about TrackMate and CellTracksColab (danio-elte.github.io/2025V4SDBStu...).

131

Reposted by Joanna Pylvänäinen

GloBIAS @globias.bsky.social · 13/01/2025

Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler. 💡 Details: www.globias.org/activities/c... 🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...

forms.gle

02522

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 10/01/2025

Yesterday we celebrated the lab's 5th anniversary (a few months late) and welcomed our new lab members 🎉🎉

0391

Reposted by Joanna Pylvänäinen

Nature Methods @natmethods.nature.com · 03/01/2025

From the Henriques lab comes NanoPyx, which optimizes bioimage analysis by dynamically selecting code variations based on input data and hardware to ensures maximum computational efficiency. www.nature.com/articles/s41...

nature.com

Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework - Nature Methods

NanoPyx optimizes bioimage analysis workflows by dynamically selecting code variations based on input data and hardware. This ensures maximum computational efficiency, enabling fast analysis of large ...

0228

Reposted by Joanna Pylvänäinen

Joachim Goedhart @joachimgoedhart.bsky.social · 16/12/2024

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

17556193

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 13/12/2024

Microscope image drifting is an everyday headache in my job. Why not try to find some beauty in it?! Also, it would be nice if microscopes were made stable 😜 #fluorescenceFriday

0130

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 13/12/2024

Sometimes, a simple message can inspire the development of a new custom image analysis tool. 🌟 Since our xCELLigence doesn't support standalone image analysis, we built one tailored to the research needs of @ivaskalab.bsky.social. github.com/CellMigratio... #Collaboration

github.com

GitHub - CellMigrationLab/PIV_4_xCELLigence: PIV analysis for xCELLigence timelapse image data

PIV analysis for xCELLigence timelapse image data. Contribute to CellMigrationLab/PIV_4_xCELLigence development by creating an account on GitHub.

272

Reposted by Joanna Pylvänäinen

eurobioimaging.bsky.social @eurobioimaging.bsky.social · 12/12/2024

📣 Many #EuroBioImaging Nodes, facilities & friends are on BlueSky🦋! Here are some to follow 🔽 @bioimaginguk.bsky.social @france-bioimaging.bsky.social @danishbioimaging.bsky.social @sln-icfo.bsky.social Don't miss the starter pack 🔽 go.bsky.app/VoeAfuN Join us - Nominate yourself or reply here!

84423

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 04/12/2024

Trying something new: For our recent preprint: Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers www.biorxiv.org/content/10.1... I made an online presentation: www.beautiful.ai/player/-ODGe...

beautiful.ai

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers

Get started with Beautiful.ai today.

44513

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 02/12/2024

Pro-tip for PIs: How to keep your lab members happy? Thanks again @guijacquemet.bsky.social 😁

1101

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 29/11/2024

Don't miss the final Postdocs in Flames Café of the year! 🔥 This Friday, join Prof. Tapani Viitala (ÅAU, UoH) on how niche research drives industrial success. 🧪📈 MediCity Seminar Room, BioCity 4th Floor. Coffee & pulla—first come, first served! ☕🍩 #PiFCafe #InFlames_flagship

030

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 25/11/2024

Don't miss the last Postdocs in Flames Café of the year this Friday! 📢 Speaker: Prof. Tapani Viitala (ÅAU,UoH) 🎯 Topic: How niche research can lead to successful industrial collaboration 📅 Fri 29 Nov, 13–14 📍 MediCity Seminar Room, BioCity 4th Floor #PiFCafé InFlames_flagship

010

Joanna Pylvänäinen @jwpylvanainen.bsky.social · 19/11/2024

Some fun adventures to wait for next year, thanks for the kind invitation @mvargam.bsky.social :)

020

Reposted by Joanna Pylvänäinen

Christophe 🔬 Leterrier @christlet.bsky.social · 15/11/2024

Check this recent talk from collaborator and pal @guijacquemet.bsky.social at UCL: fundamental cell biology tackled with cutting-edge image analysis methods www.youtube.com/watch?v=KTdZ...

youtube.com

Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep learning for microscopy

YouTube video by UCL Cell and Developmental Biology

13912

Reposted by Joanna Pylvänäinen

Nicolas Chiaruttini @nkiaru.bsky.social · 18/10/2024

Another day, another #BigDataViewer video. This time an orthoviewer + a BigVolumeViewer. Dataset = Allen Brain Atlas CCFv3. #Fiji #ImageJ All those demos will be accessible in Fiji with the PTBIOP update site soon.

03212

Reposted by Joanna Pylvänäinen

Guillaume Jacquemet @guijacquemet.bsky.social · 23/02/2024

We are looking for a Professor or Associate Professor (Level 2) in Biochemistry at @AboAkademi #Turku abo.rekrytointi.com/paikat/index... Please RT and tell your friends!! Any questions do not hesitate to ask!

035

Reposted by Joanna Pylvänäinen

Anne Carpenter @drannecarpenter.bsky.social · 17/02/2024

Register! Free webinar March 5: "Figure making best practices" by BINA (Bioimaging North America) www.bioimagingnorthamerica.org/events/figur...

bioimagingnorthamerica.org

Figure Making Best Practices - Checklists & Demo

Join the BINA Early Career WG and QUAREP-LiMi WG 12 to learn about correct and effective scientific figure making for microscopy

01511