#bioimage — Public Fediverse posts

To wrap this up: Both tools are easy to test. I highly recommend trying them on your own data to see what works best for your use case.

I’ll include #CellSeg3D in our next #Napari #bioimage analysis course (https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/). Curious what impressions and feedback the students will share. 🧪🔍

What I really like about @napari is how well it integrates modern #Python tools. Great to have such a flexible, evolving #opensource platform for (bio) #imageanalysis! 👌

If you would like to attend a microscopy or bioimage analysis training course in the next 6 months but don’t have funding, check out our Microscopy Training Grant from @J_Cell_Sci and @focalplane_jcs.

Next deadline: 6 June 2025

https://www.biologists.com/grants/jcs-focalplane-training-grants/

#Microscopy #BioimageAnalysis #Bioimage #Biology #Training #Grants

Some time ago @devTLB and I announced that we work on a review about #rstats packages for #bioimage informatics. We think it is fairly complete now.

We would be happy to get some feedback before we submit it.

Here is the link to the draft:

[Update: Copy on Codeberg]
https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf

#Bioinformatics

A gentle reminder that the deadline for registration to the True Image Deconvolution, Restoration, and Analysis Workshop is today. The workshop is virtual and free of charge.

#Bioimage #Analysis #Microscopy #Euro-Bioimaging #PSF

We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!

Software engineering intern - ...

I'm bamboozled by OMERO's APIs.

There seems to be an XML model, a Java (slice? blitz?) API that wraps the XML, a Python wrapper for that Java model (omero.model), an official high-level wrapper for that Python wrapper (omero.gateway), and a third party wrapper for that wrapper (ezomero). Then there's also a JSON API.

#ome #bioimage #omero

Some time ago, we published our #biopixR package in #JOSS

https://social.anoxinon.de/@RoedigerRG/113340746869808933

Now Tim @devTLB and I are working on our review as promised here.

https://social.anoxinon.de/@RoedigerRG/112773962698337008

The good news is, we have done most of the work on it. Now we are just polishing the paper.

We will likely share a link to a preprint server. Let's see how things evolve.

#rstats #bioinformatics #BioImage

Still amazed to have won this award! 🙌

All winners are devoted to #bioimage data, where spotting manipulation & teaching solutions is possible.

More tricky for numerical data: diverse types, summaries, complexity -> challenging to find errors/define trustworthy visuals. Lot's to do!

TOMORROW, NOV21
🏆 Meet&Greet with the winners of the #EinsteinFoundationAward
Elisabeth Bik
PubPeer's Brandon Stell,
Helena Jambor & Christopher Schmied (PixelQuality)

Register: https://www.einsteinfoundation.de/en/insights/events/award/meet-the-winners

Excellent resource to choose the correct repository to publish your #BioImage #data
in #EOSC and elsewhere:

https://zenodo-rdm.web.cern.ch/records/13945179

Thanks @EuroBioImaging !

New from a huge cast of amazing #bioimage analysts in the Journal of Cell Science - "The crucial role of bioimage analysts in scientific research and publication" journals.biologists.com/jcs/article/... . Hop into 🧵to learn more! (1/x) #bioimaging #microscopy #bioimageanalyst

The crucial role of bioimage a...

Winners of the 2024 WEHI Art of Science Exhibition were announced! You can see the whole gallery here: https://www.wehi.edu.au/art-of-science/2024/

I love this exhibition every year, and it's interesting that this year, the Still Image winner (pictured) was of the Cryo EM mist generator and not biological tissue.

#biology #bioimage #cryoem

Want to use #Python for #imageanalysis? Join the eRImote training course: "Intro to #BioImage Analysis for Life Scientists" organised by #EuroBioImaging Nodes.

🗓️Oct. 7-9

📍Sweden, France, Portugal

Innovative format w/common lectures & on-site experts.

Register⤵️

https://eurobioimaging.eu/events/intro-to-bioimage-analysis-with-python-for-life-scientists-a-distributed-in-person-training-course/

Hey! We are organizingg a #bioimage analysis #challenge!

Try your skills!!

https://focalplane.biologists.com/2024/02/26/will-your-algorithm-be-the-best-for-this-new-image-data-challenge/

> shadow.org.apache.tools.zip.Zip64RequiredException: archive contains more than 65535 entries.

It's ShadowJar time 😎

(cramming a Java codebase, all its Java dependencies, their transitive Java dependencies, their C++ dependencies, compiled C++ libraries and machine learning models into one Jar archive for some reason that remains unknown to me)

#java #bioinformatics #bioimage

#FijiSc being prepped to run on #Java 21: give it a try and please report any issues. See the post by Curtis Rueden at the image forum:
https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/1

#java21 #ImageProcessing #Bioimage

Course on "Quantitative Imaging: From Acquisition to Analysis"

Application deadline: January 31st

Course dates: April 1-16

Location: Cold Spring Harbor

Instructors: Jennifer Waters, @bethcimini @florianjug Hunter Elliott, Talley Lambert, Suliana Manley.

Financial aid is available to help offset tuition costs.

https://meetings.cshl.edu/courses.aspx?course=C-QICM&year=24

#microscopy #imaging #biology #bioimage

Do you have a #bioimage #analysis question?

Then bring it to the "Image.sc LIVE! around the world" event and a panel of image analysts will be available, live, to answer your questions and provide #ImageAnalysis support and suggestions.

January 18th (Europe, Africa, Americas)-19th (Asia, Aus, NZ) via GatherTown. Exact timetable TBA.

For more information, visit:
https://forum.image.sc/t/image-sc-live-around-the-world/89596

"Stenglein's is is one of the most pathetic works in the field of microphotography. He is one of the few who were able to achieve quite inadequate results even at low lens magnification."

#images #Bioimage 😖 😂

Read more in the first #textbook on #microscopy, in German

https://archive.org/details/b2192532x/page/254/mode/2up?view=theater&q=irre

Here is an example of using #RandomForests 🌳🌳 for #PixelClassification 🖼️ in #Python 🐍, using @napari for labeling ✍️

🌎 https://www.fabriziomusacchio.com/blog/2023-06-23-_random_forests_pixel_classifier/

#RandomForest #Napari #MachineLearning #ImageProcessing #Bioimage #BioimageAnalysis

We've just finished our course on #Bioimage Analysis with #Napari 🧠🔬, which focusses on the practical application of @napari 🩻🔧. The course material is freely available on my website. Feel free to use and share it! 😙 #OpenScience #ImageAnalysis

🌎 https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/

The BioImage Computing (BIC) workshop is open for submissions.

Where: ICCV conference in Paris.
When: October 3rd.
Submission deadline: July 21st.

Website: http://www.bioimagecomputing.com/call-for-papers/

Papers to be published with the ICCV proceedings.

Organized by Jan Funke, Anna Kreshuk, Florian Jug, Alexander Krull, Virgibie Uhlmann, Martin Weigert, Dagmar Kainmueller, Peter Bajcsy.

#BIC #BioImage #ICCV