Our end-to-end workflow for 3D pathology is now published in @NatureProtocols! This includes all the steps to go from archived pathology tissues to 3D H&E-like datasets, with an emphasis on quality control for large studies. Full text at:

A little late, but very happy to share that I have completed my PhD with @jonliu123 and am beginning a postdoc @broadinstitute in Boston! Huge thanks to all of the friends and mentors who supported me @UW. Looking forward to more 🔬 to play with and ⛰️ to hike PNW -> New England

RT @janet_sorrells: Currently recruiting graduate students in Electrical Engineering and Imaging Science! Reach out with any questions and…

@RetoPaul @jonliu123 Thank you! All possible thanks to your group's ASLM work 😊 Mainly we use fluorescent TO-PRO (nuclei) and eosin (stroma) dyes, which are then false colored to mimic the appearance of standard H&E:

Huge thanks to @LindseyBarner, @adam_k_glaser, @DavidRBrenes, and Rob for help with the optical design, for the beautiful tissue samples courtesy of Elena, Lydia, @biofizzycist , and @VaughanLabUW, and of course Larry, our friendly neighborhood pathologist!

@adam_k_glaser This Coursera from Colorado is quite good (and extensive)! You can audit for free if you go to the bottom of the individual courses: Also great glossary of key microscopy concepts from @jsdaniel02

RT @EngageScience: ⏰10 DAYS LEFT to apply to for the Engage Fall 2024 course!⏰ Submit your applications before the June 30th deadline here:…

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Awesome work on AI-triage of 3D pathology data led by @gaogan96 on deck at @CVPR next week!

@HaoYin20 @napari_imaging Laterally we are only limited by the stage scanning range and can in principle image cm-scale tissues! The max imaging depth usually depends on the optical clearing quality, which ranges from ~0.5mm (e.g. many human tissues) to many mm deep (e.g. mouse brains)

Awesome to see our 3D pathology protocol featured - we appreciate the shout out!!

Awesome event to hear from UW Grad students at Burke-Gilman Brewing on Feb 12th! 🔬🍻👇

@hego_alexandre @NatureProtocols You could teach pathologists to interpret fluorescence data, but they’ve already spent decades getting good at interpreting H&E data so we might as well make our lives easier 😊

@timdweber @NatureProtocols The render was made by @LindseyBarner using @ImarisSoftware! By adjusting the transparency of empty regions ('empty' is somewhat arbitrary) you get something between a surface rendering and a max projection - definitely the best way we've found to render these dense datasets

Huge thanks to everyone who worked on this including @LindseyBarner, @biofizzycist, @adam_k_glaser, @DavidRBrenes, @VaughanLabUW, and of course @jonliu123

@kD3AN We put together a list of resources for this a while back! See Compiled Patent Lists section:

RT @jonliu123: Check out @LindseyBarner 's final PhD paper from my lab! "AI-triaged 3D pathology to improve detection of esophageal neoplas…