🚀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
- 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).
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 !!
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
Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.
Day 5 - practising the art of tracking with @jytinevez.bsky.social and Laura Xénard.
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
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 !
Day 4, with @jytinevez.bsky.social and tracking! #neubiaspasteur2025
Coffee break in @institutpasteur.bsky.social with @strigaud.bsky.social @mambroset.bsky.social @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..
Great recipe from @cfusterbarcelo.bsky.social on how to train a DL model
Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.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
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...
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.
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
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.
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
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)
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!
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/
failed tagging you @ivanhcenalmor.bsky.social sorry!!!!
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
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.
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/...
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/...
Oh, so cool! 💫🤩
Looks amazing - congrats!!
@kbias.bsky.social Next paper? 🤪
Awesome to have @henriqueslab.bsky.social join us as a visiting professor!!!
