Robert Haase
@haesleinhuepf
Followers
11,875
Following
4,091
Media
2,799
Statuses
18,659
#GenerativeAI , LLMs, (Image) Data Analysis, GPUs @Sca_DS / @UniLeipzig , also @NFDI4BioImage , @NEUBIAS_ , @GloBIAS_ #openscience , views:mine
Leipzig, Germany
Joined August 2010
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Pinned Tweet
Teaching optics to cats, lesson 1: Refraction 😊
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🚨Game changer alert🚨 for scientists in Germany who publish and maintain
#opensource
software and
#opendata
. Our
@github
and
@ZENODO_ORG
etc repositories will be considered as publications when applying for funding
@dfg_public
🤩🚀🤯
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!
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1K
My first online
#BioImageAnalysis
lecture at the
@BIOTEC_TUD
in collaboration with
@csbdresden
and
@mpicbg
#OpenKnowledge
#OpenScience
🎓
It covers basics and an introduction to
@FijiSc
Stay tuned, I'll add lessons weekly 🥳
Enjoy!
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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!
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I just updated our
#ImageJ
#macro
#cheatsheet
and gave it a new,
#openscience
home🤓 As usual: Feedback and contributions are welcome 😃
@florianjug
#Memories
☺️ The
#ImageJ
macro cheat-sheet from the
#ScientificComputingFacility
of
@mpicbg
. It had quite some fans back in the days
#OpenTeaching
#OpenScience
🤩
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5
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509
🤫
#chatGPT
integration will be coming to
@FijiSc
's Script Editor
#SneakPreview
🥳
Thanks for the support
@ctrueden
! 🙌
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#GPUacceleration
is changing the way we do
#BioImageAnalysis
. E.g. tuning parameters of workflows becomes a completely different experience with instant feedback.
We're happy and
#soproud
to share it
#opensource
with everyone! Today out in
@naturemethods
:
#clij
🥳
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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!
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"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
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#preprint
🚨
Overwhelmed when choosing
#BioImageAnalysis
software? Read our Hitchhiker's Guide🥾
Feedback❤️ly welcome! Big thanks to the team😃
@mycroscopy
@david_legland
@mdoube
@SuperResoluSian
Ilya Belevich
@EJokitalo
Martin Schorb
@ahklemm
@tischitischer
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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
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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 🔬🖥️🌞
Congratulations Dr Pete Bankhead and Dr Robert Haase - joint winners of the RMS Award for Data Analysis in Imaging! 👏🔬🏆
Read more
@petebankhead
@haesleinhuepf
@PoLDresden
@EdinburghUni
@BioImagingUK
#BioImageAnalysis
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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
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Teaching microscopy to cats, lesson 30: imitating microscopes
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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! 🔬🖥️🚀
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38
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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 😃
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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
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Cell counting simplified 😆 with
#CellCountingArcade
for
@napari_imaging
😉🤡🎈🖥️🚀
#clesperanto
#opensource
Thanks to
@DrAnneCarpenter
and colleagues for sharing the BBBC022 data set
#openaccess
🤩
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44
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Preparing the
@cziscience
@napari_imaging
#plugin
kick-off meeting 😃 The ImageJ Macro Recorder taught thousands of biologists programming macros. I hope the [
#clesperanto
]-Assistant and the Script Editor will teach thousands of biologists
#BioImageAnalysis
with
#Python
🔬🖥️🎓💪
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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!
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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
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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
! 🤩
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My "Introduction to
@napari_imaging
" slides including some Napari plugins, User Documentation 101, and Scripting Napari using Python at
#NeubiasPasteur23
are available
#openaccess
🔬🖥️🏝️🔓
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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
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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
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#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! 🔬🤖🚀
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I got a new lab website
@PoLDresden
. 🎈My first website ever with a proper mission statement 🔬🖥️🚀💪
10
19
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Today, I gave a 3h crash course in Quantitative
#BioImageAnalysis
at
@digsbb
🔬🖥️📈
In person, jeey 😃- thanks for having me!
And as usual, you find my slides online
#OpenAccess
#OpenKnowledge
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Feeling honoured receiving this award 🥰
Big thanks to the DAIM community and
@RoyalMicroSoc
for recognizing my work in
#openscience
#BioImageAnalysis
🔬🖥️🔓
Congratulations to Robert Haase
@haesleinhuepf
(left) receiving the
@RoyalMicroSoc
Data Analysis in Imaging (DAIM) Award today at
#mmc2023UK
@RMS_EarlyCareer
@IoP_EMAG
@BioImagingUK
@JofMicroscopy
@MicroscopyViews
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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 😃
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40
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Teaching microscopy to cats, lesson 33: cleaning objectives
6
37
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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
!🤩
6
48
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I'm now officially hooked on
#LLMs
for
#BioImageAnalysis
presuming they will do my job one day. Welcome BIA-Bob! 🔬🖥️🤖
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35
200
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🏆
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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
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Teaching super-resolution microscopy to cats, lesson 99: Structured illumination
5
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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 🔬💻🤩
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29
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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 😍
6
28
175
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🔬❤️🖥️👋
8
1
175
#OpenAccess
slides of my 90 min workshop lecture about "Advanced
#BioImageAnalysis
, image data science & AI" at the Zebrafish PI meeting
#DDzebrafish22
@CRTDpress
Also big thanks to
@zoccolermarcelo
for an excellent
@napari_imaging
hands-on session🤩
4
46
172
I've uploaded my lecture about
#GenerativeAI
for
#BioImageAnalysis
to YouTube.
It covers basics behind language models,
@loicaroyer
's
@napari_imaging
-chatGPT plugin,
@langchain
and BIA-Bob. Feedback welcome! 🔬🖥️🤖🚀
5
48
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#AchievementUnlocked
🥳
My first github repository just reached 100 likes. ⭐️
Surprise: It's not a Fiji plugin, and it's no Python library.
It's our lecture materials
@tudresden_de
with
@APoetsch
@zoccolermarcelo
@jm_mightypirate
#BiAPoL
🥂
6
14
170
🚨Job alert🚨
If you're interested in interdisciplinary research between Imaging,
#BioImageAnalysis
and Machine Learning, join us as PhD student in
#BioImageDataScience
for understanding Human Pathomechanisms via
@digsbb
@PoLDresden
🔬🖥️🧠🚀
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My
#LISH22
talk slides about "3D Image Data Science with open tools" featuring
@FijiSc
@napari_imaging
@projectjupyter
#clij
#clesperanto
are available
#OpenAccess
💻🔬🚀
1
44
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My slides introducing
@napari_imaging
and the
#napariAssistant
I just gave at the
#LIBREHub
@LatamBioimaging
Workshop are available
#OpenAccess
🔬🖥️🧑🏫🔓
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My tutorial about "
#GenerativeAI
for
#BioImageAnalysis
" at
#I2K2023
will start in about 1h. Download the slides
#openaccess
:
Join the session:
🔬🖥️🤖🔓
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39
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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 🟩🦠 🖥️🧵
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38
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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 🙂
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25
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I'm thrilled, our proposal to
@agencerecherche
&
@dfg_public
was accepted🎉🍾
With
@maverof
/
@IGFLyon
,
@PavelTomancak
/
@mpicbg
and
#BiAPoL
@PoLDresden
we'll dive into the interstice between development and regeneration and further develop the Elephant and Mastodon plugins
@FijiSc
😃
10
12
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I just gave my first
@napari_imaging
tutorial at
@Sca_DS
/
@UniLeipzig
🔬🖥️🚀
As usual, all materials are
#openacces
🔓
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#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.🖖🤓
3
15
152
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 🔬🖥️📊
1
24
157
I wrote a
@focalplane_jcs
blog post about "Explorative
#ImageDataScience
in
@napari_imaging
" 🔬🖥️🎯
(Spoiler: No coding skills required)
Featuring some of my favorite plugins by
@zigutyte
@RyanSavill4
@uschmidt83
@martweig
Feedback ❤️ly welcome!
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44
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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 🖥️🔬🔓🎉
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52
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I'm sometimes* confused when designing
#BioImageAnalysis
workflows with more than 3 steps. In
@napari_imaging
I can now visualize why😄
#clesperanto
#idfg
* only very rarely🤭
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🚨
#preprint
🚨
We're bringing interactive design tools and cross-platform script-generation for Image Data Flow Graphs (
#IDFG
) to
#ImageJ
/
@FijiSc
Modify parameters of
#GPUaccelerated
operations and see how downstream images change
#clij
/
#clEsperanto
powered 🔬🖥️🚀 1/17
Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation
#bioRxiv
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42
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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!
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35
148
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
🔬🖥️🚀
0
24
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The dichroic prism on my desk is enjoying the sunny day 🌞
3
7
143
Very excited as the
#clesperanto
-assistant is among the
@napari_imaging
Plugin Accelerator projects awarded by
@cziscience
🥳
Together with
@DrLachie
🤩 and his team we will streamline designing
#BioImageAnalysis
workflows, connect to
#skimage
and
#scipy
...
11
25
145
I found a gold nugget in my overfilled inbox.
I'm so glad🥰
6
5
144
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 🔬🖥️🚀🌥️
9
5
142
Teaching academic career paths to cats, lesson 212: Signing a permanent contract
#IchBinHanna
23
2
143
Excited to be among the
@cziscience
@napari_imaging
grantees.🥳We will produce
#tutorials
about seamless integration of various plugins to solve common
#BioImageAnalysis
questions. If you know cool
#opendata
sets to analyze: pls post a link below!
🔬🖥️➡️💡
8
16
142
#TipOfTheDay
: In your grant application, between budget for
#microscopy
🔬 and
#publicationfees
📃, also request funding for professional
#BioImageAnalysis
🖼️🖥️ and
#datascience
📊🖥️ support.
You will not regret 🤓
3
38
140
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
😃🔬🖥️🚀
1
35
138
A year ago I didn't think of youtube as an efficient platform for
#BioImageAnalysis
knowledge exchange. 1234 people proved me wrong 😊
12
7
135
Jeey! 🥳 Big thanks to Anna
@APoetsch
for this joint
#BioImageAnalysis
/
#BioStatistics
/
#Python
/
#MachineLearning
teaching adventure! I had a blast!😃
Check out the links to our
#openaccess
teaching resources in the linked article⬇️🤓
#openscience
#openknowledge
Robert Haase
@haesleinhuepf
@poldresden
@csbdresden
and Anna Poetsch
@APoetsch
#MSNZ
@BIOTEC_TUD
@NCT_UCC_DD
won the Teaching Award 2021 for their outstanding joint online course on bio-image analysis & bio-statistics
@tudresden_de
. Congratulations! 🎉🏆
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14
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11
20
134
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 ⬇️⬇️⬇️
10
96
387
4
18
137
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🙏
1
46
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Dear
#BioImageAnalysis
community, dear
#nerds
🤓,
I'm writing you because of this
#job
ad posted online. I would like to apply to you for working with me in the
#BiAPoL
@PoLDresden
. We have 2
#openpositions
for image data scientists with an open mindset.
3
102
133
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😃🔬🖥️🏝️
1
28
131
Going through the
@napari_imaging
course material
@sofroniewn
provided for the
@NEUBIAS_COST
#NeubiasAcademy
yesterday makes me realize: that was the finest
#webinar
I ever attended! I also saw the huge potential in napari earlier, but I wasn't aware that future is today.🤯🤩
4
18
130
My slides about
#BioImageAnalysis
using
#LLMs
, also featuring the multi-lingual tools
#clij
,
#clesperanto
and
#biabob
are available
#openaccess
🔬🖥️🗣️🔓
Big thanks
@artgolden_
and
#iMOL
Frankfurt for hosting me!
2
26
129
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! ❤️💚💙
3
2
126
@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:
3
36
125
My mini-lecture slides about
#GenerativeAI
are available
#openaccess
🔓
Featuring some basics, applications and explaining how
@loicaroyer
's
@napari_imaging
-
#chatGPT
plugin uses
@LangChainAI
to 🤯
5
35
123
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 🧵
8
25
122
My slides for the session about on-the-fly image processing with python,
@napari_imaging
and a bit
#clesperanto
at the
#SmartMicroscopy
workshop at
@CCI_GU_SE
are online
#openaccess
😌
Thanks again
@juliafrodri
and
@camachodejay
for having me!😃
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I ordered an unusual portable computer display and I'm shocked about the quality of these devices nowadays 🤯
#augmentedreality
And yes: I'm a nerd 🤓
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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 😎
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Turning the laser on significantly improves image quality. Patent pending.
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Are you Iinterested in studying neighbor relationsships between cells in tissues? Try out napari-griottes! 🔬🖥️🍒
Great to see this out
@_hrun_
! 🎉
Napari-griottes finally made it to pypi and napari hub. 🥳 Works directly with the labels out of Cellpose in 2D or 3D. Blistering fast and easy to use.
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Gladly seeing our idea for distributing distributed (yes)
#BioImageAnalysis
using
#clij
in
@cziscience
#EOSS
program. Looking forward to work with
@StRigaud
(
@institutpasteur
),
@martinjones78
,Lucy
@EM_STP
Collinson,Amy Strange(3x
@TheCrick
) and
@PoLDresden
,
@NEUBIAS_COST
style🔬🖥️🚀
🚨
#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
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The
#autocomplete
dream for
#ImageJ
macro in
@FijiSc
became true. Update Fiji to try. Thanks to
@ctrueden
@wrasband
@jan_eglinger
@Squareys
@frauzufall
@dn_mason
Mark Hiner, Jan Brocher,
@BertrandVernay
@DataNerdery
Giovanni Cardone, Nicolás De Francesco et Al. for your support!
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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
🏝️
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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!🦠🔬🖥️🤓
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My lab turns 2 today. I'm celebrating this by adding a strong 2nd red line here 😷
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