Your microscopy news digest is here!

Twitter, microscopy forums, and bioimage analysis platforms such as image.sc, … It is difficult to keep up to date with all the discussions and news happening on the different online platforms. To address this, we have created a ‘news digest’ post to help you stay informed about what’s happening in the microscopy community.

Here is a selection of interesting news, publications and discussions that happened in the past few weeks. And a big thank you to our ‘FocalPlane reporters’: Alvaro Crevenna, Andrey Andreev, Jennifer Waters, Manish Kumar, Martin Jones, Pablo J. Sáez, and Robert Haase, who helped us create this list.

Twitter

Microscopes and imaging tools:

• A new light-sheet microscope combining deep learning to reveal 3D organelle interactions – https://twitter.com/pengfei16/…

• High-Resolution, large imaging volume, and multi-view single objective ligh-sheet microscopy. Check their video abstract too! – https://twitter.com/loicaroyer/…

• Crossbill: An open access single objective light-sheet platform – https://twitter.com/OptoManishK/…

• Field guide to 3D printing in microscopy – https://twitter.com/_mariod/…

• Controlling experimental conditions using open Arduino or Raspberry Pi – https://twitter.com/aandr314/…

• New 3D printable refractive optical elements have the potential to drastically lower the cost of phase masks used for microscopy – https://twitter.com/christlet/…

Bioimage analysis:

• Very useful cheat sheet for ImageJ – https://twitter.com/haesleinhuepf/…

• ZeroCostDL4Mic paper is out in Nature Communications – https://twitter.com/LaineBioImaging/…

• DeepImageJ updated to help make deep learning accessible to Fiji users – https://twitter.com/ArrateMunoz/…

• and DeepImageJ and ZeroCostDL4Mic working together via Bioimage Model Zoo – https://twitter.com/gomez_mariscal/…

• Steady stream of new content from NEUBIAS academy in their YouTube channel – https://twitter.com/NEUBIAS_COST/…

• Opinion paper on developing bioimage analysis – https://twitter.com/f_levet/…

• Beta testers needed for the new features of Clij2 – https://twitter.com/haesleinhuepf/…

• ABRF seeking volunteers for image analysis reproducibility study – https://twitter.com/MyABRF/…

News and interesting reads:

• Discussions on the new Zeiss SIM² – https://twitter.com/christlet/… and https://twitter.com/christlet/…

• Older tweets coming back. An interview with Manu Prakash (Foldscope) – https://twitter.com/EricTopol/…

• Online gamers becoming data analysts – https://twitter.com/TheCrick/…

• 1 year anniversary of Cell Migration Seminars + amazing time-lapse videos – https://twitter.com/pj_saez/…

• Still a few days left to enter the VolumeEM logo competition. Do you know about this new community initiative? – https://twitter.com/VolumeEM1/…

• EtchACell paper is out. Interesting citizen science project including contributions from thousands of volunteers – https://twitter.com/martinjones78/…

Hot topic: standards and metadata, the importance of data quality and reproducibility in microscopy.

• REMBI: Developing guidelines for bioimaging metadata – https://twitter.com/emblebi/…

• Guidelines on open image data tools and resources – https://twitter.com/GlobalBioImage/…

• Metadata standards for light microscopy – https://twitter.com/Ulrike_Boehm/…

• Overview of the nature of microscopy metadata and its importance – https://twitter.com/Ulrike_Boehm/…

Funding opportunities

• RFA to expand global access to bioimaging. A call for Latin America, the Caribbean, Africa, and former Soviet countries – https://twitter.com/GlobalBioImage/…

Hands-on scientists

• Hideaki Yoshimura beautiful image of the microscopy setup at work: Lasers everywhere! – https://twitter.com/Hide_Yshmr/…

• Louise Cole takes pet microscope named Violet to Imaris class – https://twitter.com/ColeLouiseUTS/…

• Ashley Ross shares with us about pain of the blank-sheet stage of writing. The worst stage! – https://twitter.com/RossLabUC/…

• Andrew Pelling shares image of post-cleanup space and calculate microscope density per sq meter – https://twitter.com/pellinglab/…

• Pablo Blinder installs a new two-photon laser – https://twitter.com/pbneurovasclab/…

Image.sc

• Christian Tischer’s paper about BigDataProcessor was published a few weeks ago. A really useful tool that has the potential to speed up image processing for many people because it reduces the amount of image data that is stored (and processed) by orders of magnitude – https://forum.image.sc/t/bigdataprocessor/34963/47

• Some minor discussions about the (quite new) QuickFigures plugin – https://forum.image.sc/t/quickfigures-a-plugin-for-building-scientific-figures-update/51399/4

• New software release for brain registration and segmentation including Napari plugins – https://forum.image.sc/t/announcing-new-ish-tools-for-whole-brain-microscopy-atlas-registration-segmentation-brainreg-brainreg-segment/53084

Discussions on building bridges:

• Inkscape – ImageJ – https://forum.image.sc/t/inkscape-bridge-extensions-for-imagej-r-processing/51264

• ZeroCostDL4Mic – ImJoy-Cellpose – https://forum.image.sc/t/zerocostdl4mic-cellpose-use-model-outside-of-collab/50875/7

Microforum

• Confocal – tricks for focusing on the slide surface – https://forum.microlist.org/t/how-to-focus-on-the-glass-surface/1407

• Hardware – looking for a bayonet mount adapter – https://forum.microlist.org/t/female-bayonet-mount-similar-to-the-one-of-nikon-eclipse-upright-microscopes/1394

• Hardware – expanding a microscope table – https://forum.microlist.org/t/cost-effective-solution-for-expanding-microscope-table-to-accomodate-additional-device/1415

• Hardware – feedback on Kinetix sCMOS camera – https://forum.microlist.org/t/kinetix-photometrics-feedback/1419

• Hardware – exchanging Olympus lenses – https://forum.microlist.org/t/looking-for-olympus-ix2-10x-and-20x-uplanfln-phase-and-ph1-annulus/1406

• An old Zeiss microscope worth buying? – https://forum.microlist.org/t/advice-for-buying-a-microscope-beginner/1410

We hope you find this post interesting. Please let us know if you think we should include other topics or discussion platforms.

If you would like to contribute to these news digest posts, contact us or join our Slack workspace.

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