Kudos,
@dfg_public
! Das ist ein wichtiger Schritt, der die zentrale Arbeit aller Kolleg:innen würdigt, die wiss. Infrastrukturen, zB Forschungsdaten-Repositorien (
@re3data
) betreiben, oder als Research Software Engineers Forschungssoftware entwickeln!
Gladly announcing: I'll join
@PoLDresden
as group leader for
#BioImageAnalysis
TechDev🥳
Together with biologists and physicists, we will dive into lakes of voxels, take off into the cloud, make 🔬 smarter, heat up GPUs, and untangle the Physics of Life😃
I'm so looking forward!
My first 24h imaging session on our custom
#XWing
scope ends with an escaping larva! :) Big respect to
@aif_cbg
and
@loicaroyer
who built and programmed this incredible machine! And big thanks to
@AnnaBajur
and
@akanksha6688
for helping me caring for these tiny beautiful animals!
"Tweeting, therefore, has the potential to disseminate scientific information widely after initial efforts to gain followers. These results should encourage scientists to invest in building a social media presence for scientific outreach." 😃
Scientists with >1000 Twitter followers reach a broader audience, including educational organizations, media, the general public and desition makers.
#SoMe4Surgery
Never click on "Apply" when changing brightness/contrast in
#ImageJ
/
@FijiSc
if you plan to analyze intensities in your images scientifically. It screws up the intensity distribution and this may lead to wrong conclusions.
#BioImageAnalysis
#TipOfTheDay
I'm deeply honoured to receive this RMS Award. And it's a huge pleasure to share it with
@petebankhead
🤩
Big thanks to
@RoyalMicroSoc
for recognizing our work with/for the
#BioImageAnalysis
community 🔬🖥️🌞
Excited to announce📢: Our proposal for the Open
#BioImageAnalysis
consortium has been selected for funding.🥳
This industry&academia joint venture will make sure that all major commercial and
#opensource
software in the field becomes directly interoperable🔬🖥️🔓
#OpenBIA
A 🧵1/5
My YouTube channel was now viewed more than 100.000 times🥳 I feel deeply honored that it became a
#BioImageAnalysis
resource.
As soon as I find time (😅) I will upload more videos, which I didn't manage to edit yet.🤞
Thanks for watching! 🔬🖥️🚀
Over the moon announcing: Effectively today I joined the Data Science Center
@Sca_DS
.AI at
@UniLeipzig
as Bio-image Data Scientist, Lecturer and Training Coordinator 🔬🖥️🚀
Thanks for the warm welcome everyone 🤗 Exciting days ahead 😃
I'm planning a
#BioImageAnalysis
video
#podcast
. Three analysts in a virtual meeting try a software/plugin/tool for 30 minutes following intuition and the user guide. No developers allowed 😉
Sounds like fun?
* Be one of the 🙋🏿🙋🏼♀️🙋♂️
* Suggest a tool we should try below⬇️
Pls RT
Did you know? After setting up an image processing workflow using the napari-assistant, you can export a
@ProjectJupyter
Notebook with Python code to reproduce and refine it 🔬🖥️🤓
Install devbio-napari to give it a try 🚀 Feedback 💚ly welcome!
Me: You shouldn't set the threshold manually, it's subjective and your choice may be hard to reproduce.
Also me: Use Otsu's thresholding method, because it looks like it performs better than Huang's.
#SeeingIsBelieving
#MeasuringIsKnowing
In February 2008 I started as student assistant
@tudresden_de
and decided to become scientist. Today I'm celebrating my 15 years work anniversary on this campus. Thanks to everyone I met along the road and who is with me at
@PoLDresden
! 🤩
Exciting news! 📢
@NEUBIAS_COST
receives funding from
@cziscience
for founding a sustainable Society for Knowledge Exchange in
#BioImageAnalysis
🎉
Big thanks to CZI, everyone involved in ✍️ and our new hosting organization
@GerBI_GMB
😃
🔬🖥️🥳
Read more:
We’re also supporting collaborative projects that are
#ImagingTheFuture
by accelerating the dissemination & adoption of cutting-edge imaging technologies, methods, platforms and training resources
Fascinated watching 62 hours of Tribolium embryo development, nuclei-GFP marked, prepared by
@akanksha6688
, imaged in our light-sheet
#XWingScope
, depth-color projected from two views. Wonderful images are acquired in wonderful research environments
@aif_cbg
@csbdresden
@mpicbg
#biabob
0.9.0 is out! It Enables you to program basic
#BioImageAnalysis
in English instead of Python.😃
It's an exciting experiment, similar to OpenAI's Data Analyst, but
#opensource
🥳
Feedback 💚ly welcome! 🔬🤖🚀
I just released a little
@napari_imaging
#plugin
for simplifying my life and maybe also of others who like click-and-run
#BioImageAnalysis
: "napari-segment-blobs-and-things-with-membranes"😌
Feedback 💚welcome 😃
The new
#TrackMate
#preprint
is truly amazing. It now offers support for segmenting blobs and linking them via overlap. And of course, it is easily extensible (awesome!). It took me 3hrs to write a TrackMate-
#clij2
plugin. Fantastic work by Dmitry Ershov et al. and
@jytinevez
!🤩
Drosophila embryo (histone-RFP)
#lightsheet
imaging onset of gastrulation
Post-proccesing (DoG, cylind.-max-Proj, spot-detection) of 300 frames takes:
#ImageJ
on a laptop CPU:
2:44 h 🙄
#ImageJ
+
#clij
on the same laptop with built-in
@Intel
GPU:
11 min🏆
The new release of napari-accelerated-pixel-and-object-classification brings the long-awaited code generation for improved
#reproduciblescience
🔬🖥️🚀
pip install napari-accelerated-pixel-and-object-classification==0.14.1
I implemented an oldie-but-goodie for Jupyter Notebooks: Interactive plotting and clustering with segmented images side-by-side; new in
#stackview
0.7.11: "clusterplot", inspired by the napari-clusters-plotter 🔬💻🤩
Perfect timing 😃- Serosa rupture of
#Tribolium
castaneum embryo filmed just before it escaped.
Thanks
@happifocus
for setting this experiment up and programming the
#SmartMicroscope
- the result looks so beautiful 😍
I just handed over the key to my flat and beautiful backyard (Fig. 1). I came to this city to study in 2006, stayed for a PhD, did a postdoc or two, and lead a group. With all highs and lows, I had a fantastic time here.😌😃
Big thx to Dresden's amazing research community🔬❤️🖥️👋
What if we could do
#BioImageAnalysis
on the level of grids of cells the same way we process grids of pixels using filters?🙃
My article in
@FrontiersIn
is out! 🥳
I was super excited when writing about it. I hope you enjoy reading!🤓
A 🟩🦠 🖥️🧵
Dear
#PIs
and senior staff,
please follow safety measures, also if it doesn't seem really necessary. Your mentees might be in
#riskGroups
. And they may not speak up. You need to be a good example in order to protect them. Thanks 🙂
#BioImageAnalysis
with
#Python
#protip
: Instead of writing super-programs and -scripts that can do everything for you, program tiny, well-documented, reusable and intuitive functions. Prototype them in notebooks, collect them in a library and make them live long and prosper.🖖🤓
Thanks to Kevin
@ky396
Yamauchi et. al.'s excellent work on 3D interactivity in
@napari_imaging
, I was able to update napari-skimage-regionprops to bring you this
#BioImageAnalysis
visualization/interactivity sugar 🔬🖥️📊
It's a wrap!I had a blast in my first semester teaching
@UniLeipzig
/
@Sca_DS
.AI: Microscopy Research Data/Software Management,
#BioImageAnalysis
, Napari,
#LLMs
.
All materials are online
#openaccess
: about 800 PPT slides + 100 Jupyter Notebooks 🖥️🔬🔓🎉
You can now
#AI
-generate entire Juypter Notebooks for your
#BioImageAnalysis
tasks with the new release 0.15.0 of
#biabob
🔬🖥️🗒️🎉
pip install bia-bob==0.15.0
As usual, feedback 💚ly welcome!
I just uploaded my [annual] lecture slides about "Current challenges in GPU-accelerated image processing for the life sciences" hosted by
@GuidoJuckeland
in his lecture series on Highly Parallel Computing using GPUs
@tudresden_de
#openaccess
🔬🖥️🚀
I just submitted this 30 page PDF the German way. 😌
If the response is positive, there will be a party 🥳 and then we'll push
#BioImageAnalysis
and
#DataScience
one level up 🔬🖥️🚀🌥️
Your
#ImageJ
Macro takes ages to analyze your images and your graphics card is idle? Learn how to speed up your
#BioImageAnalysis
macro and how to use
#clij
in this chapter I happily wrote together with
@happifocus
😃🔬🖥️🚀
Bold statement "Transformers do not outperform Cellpose" by Stringer & Pachitariu 😯
No matter how this controversy ends, this preprint is a fantastic read to learn about good scientific practice in cell segmentation method comparison studies 🤩
#Cellpose
remains the state-of-the-art for cellular segmentation. See our new paper, in response to Ma et al, Nat Methods 2024.
Paper:
Leaderboard results ⬇️⬇️⬇️
Dear fans of
#GPUaccelerated
#BioImageAnalysis
in
@FijiSc
,
It's my pleasure to announce that
#clij
2.5.0.0-BETA is out for testing🥳
I need your help! Please help testing the new features so that we can safely release the update to everyone mid June.THX🙏
I'm so happy to see the
@napari_imaging
#clesperanto
assistant working with timelapse data, e.g. for segmenting dividing nuclei. It was quite a bit work😌
New pre-release 0.9.5 is out!🥳Early adopters are welcome to try. Let me know what you think😃🔬🖥️🏝️
I think I wrote a thousand scripts back in my days as core facility engineer. 🔬💻🤓
Sometimes users come back to me like this. You can't imagine how much that means to me! ❤️💚💙
Happily announcing the first alpha-release of
#clij2
! 🥳Compared to
#clij
it comes with 146 new operations for label maps, point clouds, meshes, adv. measures, new filters and more!🔬💻🚀
Early adopters and experimentalists are welcome to try! I❤️feedback!
@HenriquesLab
There was recently an announcement of QuickFigures, an
#ImageJ
/
@FijiSc
plugin for drafting Figures. It comes with a preprint and looks already stunning 🤯
Forum:
#preprint
:
Demo:
How to create icons on your Windows Desktop that start your favorite Python tools such as
@napari_imaging
and
@ProjectJupyter
in specific conda environments.
A short 🧵
The family of [GPU-]Accelerated Pixel and Object Classifiers (APOC) is growing. Please welcome the Object-Selector and the Object-Merger to the party!🔬🖥️🚀🥳
Also new: The graphical abstract below can be reproduced using
@ProjectJupyter
Notebook 😎
🚨
#OpenSource
tools are the invisible foundation of biomedicine. That’s why we’re continuing to support open source software projects essential for scientists. Learn more about our grantees
Happy Birthday
#clij
,
we had an amazing year since your first stable release🥳
It's now time for deprecating, handing over to
#clij2
and watching it processing images of cells and tissues
#GPUaccelerated
at light speed. 🔬💻🚀
Next stop:
#clEsperanto
🏝️
I wrote a
@focalplane_jcs
blog post about working on
#BioImageAnalysis
scripts collaboratively with others using
@github
.
If you're a life-scientist with scripting skills who never used
#git
before, that one is written for you.
Feedback 💚 welcome!🦠🔬🖥️🤓