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@Co_BiologistsIf 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 <a href="https://biologists.social/@J_Cell_Sci" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@J_Cell_Sci</a> and <a href="https://biologists.social/@focalplane_jcs" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@focalplane_jcs</a>. Next deadline: 6 June 2025<a href="https://www.biologists.com/grants/jcs-focalplane-training-grants/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biologists.com/grants/jcs-focalplane-training-grants/</a><a href="https://biologists.social/tags/Microscopy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Microscopy</a> <a href="https://biologists.social/tags/BioimageAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioimageAnalysis</a> <a href="https://biologists.social/tags/Bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioimage</a> <a href="https://biologists.social/tags/Biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Biology</a> <a href="https://biologists.social/tags/Training" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Training</a> <a href="https://biologists.social/tags/Grants" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Grants</a>

devSJR :python: :rstats:Some time ago <a href="https://mastodon.social/@devTLB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@devTLB</a> and I announced that we work on a review about <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> packages for <a href="https://fosstodon.org/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> 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] <a href="https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf</a><a href="https://fosstodon.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a>

NFDI4BIOIMAGEExiting news! 💥 We'll be attending the Helmholtz Imaging Conference in Potsdam, June 25-27.Our <a href="https://nfdi.social/@nfdi4bioimage" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@nfdi4bioimage</a> Task Area Leader <a href="https://mastodon.social/@haesleinhuepf" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@haesleinhuepf</a> from <a href="https://wisskomm.social/@unileipzig" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@unileipzig</a> will present a keynote on "Large Language Models for <a href="https://nfdi.social/tags/BioImage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioImage</a> Data Science". In addition, Riccardo Massei from <a href="https://helmholtz.social/@ufz" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@ufz</a> will offer a workshop on "Advances and challenges in zebrafish image and video analysis". We are looking forward to meeting you there and to the exciting program!👉 Registration: <a href="https://events.hifis.net/event/2061/overview" rel="nofollow noopener noreferrer" target="_blank">https://events.hifis.net/event/2061/overview</a>

Nadia HalidiA 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.<a href="https://mathstodon.xyz/tags/Bioimage" class="mention hashtag" rel="tag">#Bioimage</a> <a href="https://mathstodon.xyz/tags/Analysis" class="mention hashtag" rel="tag">#Analysis</a> <a href="https://mathstodon.xyz/tags/Microscopy" class="mention hashtag" rel="tag">#Microscopy</a> <a href="https://mathstodon.xyz/tags/Euro" class="mention hashtag" rel="tag">#Euro</a>-Bioimaging <a href="https://mathstodon.xyz/tags/PSF" class="mention hashtag" rel="tag">#PSF</a>

c4r510Linking metadata in electronic lab notebook <a href="https://mastodon.world/tags/OpenBIS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenBIS</a> with metadata in the <a href="https://mastodon.world/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> resource <a href="https://mastodon.world/tags/Omero" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Omero</a>: How many images are present in omero for a given sample in OpenBIS? At <a href="https://mastodon.world/tags/mpievolbio" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#mpievolbio</a>, to answer this and similar questions, we map both resources to <a href="https://mastodon.world/tags/RDF" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RDF</a> <a href="https://mastodon.world/tags/KnowledgeGraphs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#KnowledgeGraphs</a> using the <a href="https://mastodon.world/tags/ontop" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ontop</a> framework, serve the materialized <a href="https://mastodon.world/tags/KGs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#KGs</a> via <a href="https://mastodon.world/tags/qLever" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#qLever</a> (<a href="https://qlever.cs.uni-freiburg.de" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://qlever.cs.uni-freiburg.de</a>) and run a <a href="https://mastodon.world/tags/SPARQL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SPARQL</a> query. Answered in no time! @nfdi4bioimage <a href="https://mastodon.world/tags/LinkedOpenData" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#LinkedOpenData</a> <a href="https://mastodon.world/tags/FAIR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#FAIR</a> <a href="https://mastodon.world/tags/MicrobialPopulationBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MicrobialPopulationBiology</a> @ontop

multimericI'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.<a href="https://genomic.social/tags/ome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ome</a> <a href="https://genomic.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> <a href="https://genomic.social/tags/omero" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#omero</a>

RoedigerRGSome time ago, we published our <a href="https://social.anoxinon.de/tags/biopixR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biopixR</a> package in <a href="https://social.anoxinon.de/tags/JOSS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#JOSS</a><a href="https://social.anoxinon.de/@RoedigerRG/113340746869808933" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://social.anoxinon.de/@RoedigerRG/113340746869808933</a>Now Tim <a href="https://mastodon.social/@devTLB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@devTLB</a> and I are working on our review as promised here.<a href="https://social.anoxinon.de/@RoedigerRG/112773962698337008" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://social.anoxinon.de/@RoedigerRG/112773962698337008</a>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.<a href="https://social.anoxinon.de/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://social.anoxinon.de/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://social.anoxinon.de/tags/BioImage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioImage</a>

Helena Klara JamborStill amazed to have won this award! 🙌 All winners are devoted to <a href="https://mastodon.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> 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 <a href="https://mastodon.social/tags/EinsteinFoundationAward" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EinsteinFoundationAward</a> Elisabeth Bik PubPeer's Brandon Stell, Helena Jambor & Christopher Schmied (PixelQuality)Register: <a href="https://www.einsteinfoundation.de/en/insights/events/award/meet-the-winners" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.einsteinfoundation.de/en/insights/events/award/meet-the-winners</a>

Guillaume GayExcellent resource to choose the correct repository to publish your <a href="https://biologists.social/tags/BioImage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioImage</a> <a href="https://biologists.social/tags/data" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#data</a> in <a href="https://biologists.social/tags/EOSC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EOSC</a> and elsewhere:<a href="https://zenodo-rdm.web.cern.ch/records/13945179" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://zenodo-rdm.web.cern.ch/records/13945179</a>Thanks <a href="https://mastodon.social/@EuroBioImaging" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@EuroBioImaging</a> !

multimericWinners of the 2024 WEHI Art of Science Exhibition were announced! You can see the whole gallery here: <a href="https://www.wehi.edu.au/art-of-science/2024/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.wehi.edu.au/art-of-science/2024/</a>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.<a href="https://genomic.social/tags/biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biology</a> <a href="https://genomic.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> <a href="https://genomic.social/tags/cryoem" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoem</a>

EuroBioImagingWant to use <a href="https://mastodon.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> for <a href="https://mastodon.social/tags/imageanalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#imageanalysis</a>? Join the eRImote training course: "Intro to <a href="https://mastodon.social/tags/BioImage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioImage</a> Analysis for Life Scientists" organised by <a href="https://mastodon.social/tags/EuroBioImaging" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EuroBioImaging</a> Nodes. 🗓️Oct. 7-9📍Sweden, France, Portugal Innovative format w/common lectures & on-site experts. Register⤵️<a href="https://eurobioimaging.eu/events/intro-to-bioimage-analysis-with-python-for-life-scientists-a-distributed-in-person-training-course/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://eurobioimaging.eu/events/intro-to-bioimage-analysis-with-python-for-life-scientists-a-distributed-in-person-training-course/</a>

NFDIWhat role does NFDI play for different disciplines? Our series continues with Stefanie Weidtkamp-Peters of <a href="https://nfdi.social/@nfdi4bioimage" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@nfdi4bioimage</a> ℹ NFDI4Bioimage works on building an infrastructure of bioimaging data and supporting researchers in handling, storing, reusing and sharing data. 💡 More about NFDI4Bioimage: <a href="https://lnkd.in/eB3VFQrv" rel="nofollow noopener noreferrer" target="_blank">https://lnkd.in/eB3VFQrv</a>ℹ Learn more about the NFDI consortia <a href="https://lnkd.in/ejvBb7mu" rel="nofollow noopener noreferrer" target="_blank">https://lnkd.in/ejvBb7mu</a><a href="https://nfdi.social/tags/fdm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#fdm</a> <a href="https://nfdi.social/tags/rdm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rdm</a> <a href="https://nfdi.social/tags/nfdi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nfdi</a> <a href="https://nfdi.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> <a href="https://nfdi.social/tags/researchdata" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#researchdata</a>

Guillaume GayHey! We are organizingg a <a href="https://biologists.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> analysis <a href="https://biologists.social/tags/challenge" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#challenge</a>! Try your skills!!<a href="https://focalplane.biologists.com/2024/02/26/will-your-algorithm-be-the-best-for-this-new-image-data-challenge/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://focalplane.biologists.com/2024/02/26/will-your-algorithm-be-the-best-for-this-new-image-data-challenge/</a>

multimeric> 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)<a href="https://genomic.social/tags/java" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#java</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a>

Albert Cardona<a href="https://mathstodon.xyz/tags/FijiSc" class="mention hashtag" rel="tag">#FijiSc</a> being prepped to run on <a href="https://mathstodon.xyz/tags/Java" class="mention hashtag" rel="tag">#Java</a> 21: give it a try and please report any issues. See the post by Curtis Rueden at the image forum: <a href="https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/1" target="_blank" rel="nofollow noopener noreferrer" translate="no">https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/1</a><a href="https://mathstodon.xyz/tags/java21" class="mention hashtag" rel="tag">#java21</a> <a href="https://mathstodon.xyz/tags/ImageProcessing" class="mention hashtag" rel="tag">#ImageProcessing</a> <a href="https://mathstodon.xyz/tags/Bioimage" class="mention hashtag" rel="tag">#Bioimage</a>

Albert CardonaCourse on "Quantitative Imaging: From Acquisition to Analysis"Application deadline: January 31stCourse dates: April 1-16Location: Cold Spring HarborInstructors: Jennifer Waters, <a href="https://fediscience.org/@bethcimini" class="u-url mention">@bethcimini</a> <a href="https://mastodon.online/@florianjug" class="u-url mention">@florianjug</a> Hunter Elliott, Talley Lambert, Suliana Manley.Financial aid is available to help offset tuition costs.<a href="https://meetings.cshl.edu/courses.aspx?course=C-QICM&year=24" target="_blank" rel="nofollow noopener noreferrer" translate="no">https://meetings.cshl.edu/courses.aspx?course=C-QICM&year=24</a><a href="https://mathstodon.xyz/tags/microscopy" class="mention hashtag" rel="tag">#microscopy</a> <a href="https://mathstodon.xyz/tags/imaging" class="mention hashtag" rel="tag">#imaging</a> <a href="https://mathstodon.xyz/tags/biology" class="mention hashtag" rel="tag">#biology</a> <a href="https://mathstodon.xyz/tags/bioimage" class="mention hashtag" rel="tag">#bioimage</a>

QuokkaDo you have a <a href="https://scicomm.xyz/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> <a href="https://scicomm.xyz/tags/analysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#analysis</a> 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 <a href="https://scicomm.xyz/tags/ImageAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ImageAnalysis</a> support and suggestions.January 18th (Europe, Africa, Americas)-19th (Asia, Aus, NZ) via GatherTown. Exact timetable TBA.For more information, visit: <a href="https://forum.image.sc/t/image-sc-live-around-the-world/89596" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://forum.image.sc/t/image-sc-live-around-the-world/89596</a>

Helena Jambor 💔 🇮🇱 🇺🇦"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."<a href="https://vis.social/tags/images" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#images</a> <a href="https://vis.social/tags/Bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioimage</a> 😖 😂 Read more in the first <a href="https://vis.social/tags/textbook" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#textbook</a> on <a href="https://vis.social/tags/microscopy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#microscopy</a>, in German<a href="https://archive.org/details/b2192532x/page/254/mode/2up?view=theater&q=irre" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://archive.org/details/b2192532x/page/254/mode/2up?view=theater&q=irre</a>

Fabrizio MusacchioHere is an example of using <a href="https://sigmoid.social/tags/RandomForests" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RandomForests</a> 🌳🌳 for <a href="https://sigmoid.social/tags/PixelClassification" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PixelClassification</a> 🖼️ in <a href="https://sigmoid.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> 🐍, using <a href="https://fosstodon.org/@napari" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@napari</a> for labeling ✍️🌎 <a href="https://www.fabriziomusacchio.com/blog/2023-06-23-_random_forests_pixel_classifier/" rel="nofollow noopener noreferrer" target="_blank">https://www.fabriziomusacchio.com/blog/2023-06-23-_random_forests_pixel_classifier/</a><a href="https://sigmoid.social/tags/RandomForest" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RandomForest</a> <a href="https://sigmoid.social/tags/Napari" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Napari</a> <a href="https://sigmoid.social/tags/MachineLearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MachineLearning</a> <a href="https://sigmoid.social/tags/ImageProcessing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ImageProcessing</a> <a href="https://sigmoid.social/tags/Bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioimage</a> <a href="https://sigmoid.social/tags/BioimageAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BioimageAnalysis</a>

Fabrizio MusacchioWe've just finished our course on <a href="https://sigmoid.social/tags/Bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioimage</a> Analysis with <a href="https://sigmoid.social/tags/Napari" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Napari</a> 🧠🔬, which focusses on the practical application of <a href="https://fosstodon.org/@napari" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@napari</a> 🩻🔧. The course material is freely available on my website. Feel free to use and share it! 😙 <a href="https://sigmoid.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> <a href="https://sigmoid.social/tags/ImageAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ImageAnalysis</a>🌎 <a href="https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/" rel="nofollow noopener noreferrer" target="_blank">https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/</a>

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