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Reposted by Joanna Pylvänäinen

Turku BioImaging @turkubioimaging.bsky.social · 4d

🚀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

jobs.helsinki.fi

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Guillaume Jacquemet @guijacquemet.bsky.social · Jul 1

- 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).

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 !!

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Reposted by Joanna Pylvänäinen

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 !!

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Reposted by Joanna Pylvänäinen

Elnaz @mycroscopy.bsky.social · May 28

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

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 16

Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 16

Day 5 - practising the art of tracking with @jytinevez.bsky.social and Laura Xénard.

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Reposted by Joanna Pylvänäinen

Stéphane Rigaud @strigaud.bsky.social · May 15

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

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Stéphane Rigaud @strigaud.bsky.social · May 15

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 !

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 15

Day 4, with @jytinevez.bsky.social and tracking! #neubiaspasteur2025

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 14

Coffee break in @institutpasteur.bsky.social with @strigaud.bsky.social @mambroset.bsky.social @gaellel.bsky.social ☕️

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Reposted by Joanna Pylvänäinen

Gaëlle Letort @gaellel.bsky.social · May 13

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..

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 13

Great recipe from @cfusterbarcelo.bsky.social on how to train a DL model

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Reposted by Joanna Pylvänäinen

Stéphane Rigaud @strigaud.bsky.social · May 13

Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · May 13

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

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Benjamin Judkewitz @benjulab.bsky.social · May 12

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...

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Reposted by Joanna Pylvänäinen

GloBIAS @globias.bsky.social · Apr 28

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.

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Reposted by Joanna Pylvänäinen

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Apr 8

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

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Reposted by Joanna Pylvänäinen

Journal of Cell Science @jcellsci.bsky.social · Apr 14

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.

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Apr 7

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

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · Apr 8

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!

Guillaume Jacquemet @guijacquemet.bsky.social · Apr 7

Here we share our opinions on "Practical considerations for data exploration in quantitative cell biology"
journals.biologists.com/jcs/article/...

Joanna, Hanna and I worked quite a bit on this piece and I hope you find it useful
Many thanks to @jcellsci.bsky.social for publishing it

Practical considerations for data exploration in quantitative cell biology

Summary: We present practical guidelines for data exploration in quantitative cell biology that are designed to help yield reliable conclusions and promote a collaborative, transparent approach to dat...

journals.biologists.com

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Reposted by Joanna Pylvänäinen

Lars-Anders Carlson @lacarlson.bsky.social · Apr 4

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/

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · Apr 1

failed tagging you @ivanhcenalmor.bsky.social sorry!!!!

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Joanna Pylvänäinen @jwpylvanainen.bsky.social · Apr 1

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

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Journal of Cell Science @jcellsci.bsky.social · Mar 20

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.

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