21 Jul 2023
This award goes to ALL authors and I must send out ❤️ and 🙏 to Martin (@martweig) who really is the 🧠 behind CARE and Uwe (@uschmidt83) without who the quality and usability of CSBDeep would not be anywhere close to what it is. @PavelTomancak helped us write a GOOD paper, and…
21 Jul 2023
Congratulations to @florianjug for being awarded the 2023 ICBS Frontiers of Science award! The International Congress for Basic Science honors top research with an emphasis on achievements from the past 5 years which are both excellent and of outstanding scholarly value.
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As part of CAM/NIC teaching activities @NUFeinbergMed @NU_CDB our in-house expert image analyst David Kirchenbuchler gave a tour-de-force course covering image analysis. @FijiSc @NikonInst #Noise2Void @florianjug #CARE #CSBDeep #TensorFlow #WekaSegmentation #PCA A great teacher!
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GitHub stats give adequate credits to the creators of this truly wonderful resource: @frauzufall (lion share) and @bewilh.
github.com/CSBDeep/CSBDeep_f…
Thanks to you two and also to all other (beyond Fiji) CSBDeep heroes!
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28 Jul 2021
Just got the numbers, 13838 users had the CSBDeep update site enabled on @FijiSc since 2017. Good job @jug_lab @florianjug
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18 May 2021
This weeks #ImageAnalysis tool is CSBDeep; a deep learning toolbox for microscopy image restoration and analysis. csbdeep.bioimagecomputing.co…
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30 Apr 2021
If you’re looking for a friendly interface to interact with code, notebooks such as @ProjectJupyter or @GoogleColab notebooks are a great resource.
#CSBDeep, #ZerocostDL4Mic and #CellPose prepared ready-to-use notebooks to test and/or train neural networks.
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30 Apr 2021
Plugins such as #CSBDeep, #DeepImageJ, and #DeepMIB integrate deep learning into common image analysis toolboxes.
These plugins are a great option for those familiar with #ImageJ @Icy_BioImaging #MicroscopyImageBrowser
@ilastik_team also has deep learning tools (in beta now)
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10 Mar 2021
Thank you @pushkal_sharma
I'm afraid that you'll need to train/fine-tune a model, BUT that's not a problem any more if you have some annotated images: #ZeroCostDL4Mic is your solution. Also you can try to train #DenoiSeg in the #CSBDeep plugin for ImageJ, or use #Ilastik, #Yapic
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24 Dec 2020
Don’t worry, both are from @FijiSc‘s CSBDeep... 😉 @frauzufall @jug_lab
The Noisepecker is the pet of the GPU Heavy Lifter...
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24 Dec 2020
24 Jul 2020
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1 Dec 2020
The #i2k2020 phenotype: 10:30 PM roaming around the island, having a beer, updating CUDA, training a network and labelling images. Good thing I expected nothing less...
#CSBDeep #WeAreStarDist
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24 Nov 2020
Thanks Pedro! It's really fun and the DL approaches are amazingly powerful. Especially the #CARE networks by @martweig. The implementation in #ZeroCostDL4Mic and the #CSBDeep plugin in #Fiji are super nice to use! Thanks to the entire #OpenSource #DeepLearning community!
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20 Nov 2020
Only possible with the help of the Heilemann @henriqueslab @seamus_holden @guijacquemet labs and the awesome #OpenSource philosophy of the DL community! #ZeroCostDL4Mic #CSBDeep #FijiSc
Source for the car AI video: tesla.com/autopilotAI
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11 Oct 2020
#I2K. 2x4 hour tutorials on #ImgLib2 #BDV #Numpy #Weka #CellPose #N5 #ImageJ2 #Ilastik #CLIJ #ImJoy #mManager #OMERO #ITK #SciView #CellProfiler #Icy #CSBDeep #CARE #StarDist #Noise2Void #BigStitcher Missing something? Respond to invite or apply. Oct 25th
janelia.org/you-janelia/conf…
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26 Aug 2020
Just wanted to mention that CSBDeep (the framework of StarDist) already supports processing in chunks 😉
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24 Jul 2020
New tool available on the CSBDeep @FijiSc update site:
DenoiSeg - joint denoising and segmentation method based on #N2V and #CSBDeep by @tibuch_ @Mangal_Prakash_ @sagzehn @florianjug.
Details: forum.image.sc/t/denoiseg-jo…
Preprint: arxiv.org/abs/2005.02987
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14 Jul 2020
New back-to-back releases of our DL python packages csbdeep and stardist. Among many other things, now allows for using tf2, stitched predictions on large 2D images, and importing 3D stardist results in @blender_org
:) kudos to @uschmidt83!
14 Jul 2020
New Python releases for #CSBDeep and #StarDist! Lots of improvements under the hood, including support for TensorFlow 2. Joint effort with @martweig!
All changes:
github.com/CSBDeep/CSBDeep/r…
github.com/mpicbg-csbd/stard…
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14 Jul 2020
However Stardist/csbdeep models trained with tf 2 should already run with the current Fiji plugin when using the tf 1.14 backend
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