International Informal
Microscopy Hour

• comparing SimpleITK and ANTs
• running linux-only code on Windows throug windows subsystem for linux
• photodamage and optimizing laser power
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449752/
• https://elifesciences.org/articles/53205
• red-shifted indicators
• https://pubs.acs.org/doi/10.1021/jacs.9b06092
• not every newest GCaMP is the best; some stick with GCaMP5
• example of 3D registration: https://www.sciencedirect.com/science/article/pii/S2211124722015194
• suite2P, CaImAn etc - what to pick?
• manual registration via itk-SNAP http://www.itksnap.org/pmwiki/pmwiki.php
• whats the difference / when to use nuclear-localized vs cyto- GCaMPs
• image artifacts affect on registration

• Getting started at working at the core
• Comparing custom and commercial systems
• Data using USB drives vs writing directly to network storage
• How writing data via network can corrupt your experiment data
• Compression through JetRaw
• Running fiber/copper in the walls
• Custom scopes: photodamage becomes a thing to consider as experiments get more complicated
• Using automatic scripts to delete data after 30 days helps users' morale
• Use TreeView software to get overview of where data is saved
• Analog for mac os: Disk Inventory X
• Managing Windows, e.g. setting up PageFile size way below RAM
• PCIe NVMe storage for users who need 100fps / up to 2GB/s for fast acquisition
• Buying servers: ask for academic discount
• Aging of hardware/computers: things can run for 10-12 years with no issues; beware plastic parts that wear out
• Long-living policies that work well
• A lot of necessary "service" is de-oiling and de-dusting
• Replacing gears / parts using 3D printing or CNC?
• Finding replacement/repair after-market service
• Wheeling and dealing: purchasing, quotes, and vendors

After short presentations we got to covering topics:

• Why do you like/wanted to work at a microscopy core?
• What is required to "get into microscopy?"
• What knowledge/skills make biologists' life easier in microscopy?
• Shortening the loop between acquisition and analysis
• Math is not scary
• Image is a bunch of numbers, not "a picture"
• Users care about numbers and data, not about light rays and optics (that is what microscopists/builders care about)
• Data management. Compressing images into JPG and deleting originals to save space...
• Calculating required data before experiments start
• Learning materials: link.springer.com/book/10.1007/978-3-030-22386-1 and iBiology digital image analysis
• Imaging ONEWORLD looking for co-organisers: rms.org.uk/events/imaging-oneworld-series.html
• Data management: local infra and users' behavior is often the bottleneck
• Some data that never will be analyzed/used, shift responsibility for data & analysis on users/biologists because it's only fair way
• Work in facilities: how does the job split between servicing (scopes & users), building custom stuff, analysis, teaching...
• How facilities differ based on size/location
• Growing in facility; difference between custom and commercial
• Types of facility users and how to help them
• Work in industry vs work in academia; freedom etc
• Facility size & impact magnitude; microscopists can have real impact by spending not that much time, especially in smaller facilities
• Interviewing for a job in facility: talk to managers AND users
• Best advice for microscopy newbies: ask the technician!
• Basic reading: consult with colleagues, read papers specific to your sample, Lakowicz
• Regular plug of image.sc for image analysis and microlist.org for everything
• "Art of keeping data honest" — bitesizebio.com/30308/quantify-images-unbiased-way/ and embopress.org/doi/full/10.15252/embj.2020105889
• Expansion microscopy (suddenly :)
• Image analysis is extension of biology experiment; honest microscopy is keeping imaging params the same, and varying single param in biology

• @ReynaudEmmanuel reminds us about "metrology suitcase"; slide from @BioimagingNA
• Trusting hardware & doubting old hardware
• Piezo stages (and issues thereof)
• Talking to microscopy companies efficiently
• Grants & service contracts
• Data management / transfer
• Onboarding new users to light-sheet
• Core director's role
• Helping users start (use smallest FOV / sample), troubleshoot samples
• Getting info from paper vs from the authors directly
• How to get software part of paper working
• Clearing protocols
• Spilled (clearing) chemicals and smells
• How to manage expectations of PI about the experiments
• FRET, 2P-FRET & FLIM-FRET
• Consulting first-timers: really need to collaborate on definition of project, goals, pick methods. Core is not "plug-and-play"
• CZI funding feel in the need for custom but user-friendly systems
• Onboarding users on custom setups
• Development of commercial system