The Imaging and Optics Facility would like to help you to spend your forced off-campus time efficiently. To that extent we would like to share the following resources with you (this list will be continuously updated):
→ The Imaging and Optics Facility would like to acknowledge all of the authors of the cited and linked resources for making their resources available for the community!
FEATURED CONTENT:
[24-08-2020] FLIMj: an open-source ImageJ toolkit for fluorescence lifetime image data analysis. just released in bioarchive; github and ImageJ.MICROSCOPY
MICROSCOPY LEARNING PLATFORMS – the following websites provide learning platforms with background information about different microscopy basics and technologies
- MicroscopyU (Nikon)
- Microscopy Resource Center (Olympus)
- Technical resources (Thorlabs)
- Science-lab (Leica)
- Zeiss Campus (Zeiss)
MICROSCOPY – FREE ONLINE BOOKS
- Digital Image Processing: Part II H Zhou, J Wu, J Zhang – 2010 (Ventus Publishing)
- Image Processing: principles and applications T. Acharya & A.K. Ray – 2005 (Wiley)
- Fundamentals of Image Processing I.T. Young; J.J. Gerbrands & L.J. v Vliet – 2004 (via Researchgate)
- BOOKS FROM IST LIBRARY – (big !thank you! to the IST Library)
– Imaging and Spectroscopic Analysis of Living Cells
Edited by P.Michael Conn
– Cell Biologcal Applications of Confocal Microscopy vol.38
Edited by Brian Matsumoto
– Cell biological applications of confocal microscopy vol 70
Edited by Brian Matsumoto
– Laser Scanning Microscopy and Quantitative Image Analysis of Neuronal Tissue Edited by
MICROSCOPY – ONLINE SEMINARS
- iBiology Online seminar series: iBiology microscopy-series
- Photometrics offers a Remote learning seminars: online registration
- Royal Microscopical Society offers online Microscopy Talks: Connect, learn and stay up to date
- PicoQUANT free webinar series for technical background for quantitative imaging
MICROSCOPY – please follow the links to find more information about the listed topics
- Basic introduction (Zeiss);
- Microscopy basics (Photometrics)
- Image formation (Zeiss)
- Guidelines for Best Practices in Image Processing
- Illumination: Köhlering (Photometrics)
- Sampling: Nyquist calculator (SVI)
- Objectives: high performance objectives by Zeiss
- Cameras and scanning detectors:
- …
MICROSCOPY MAINTENANCE & CLEANING OPTICS
- How to clean objectives, according to Nikon protocol
- Removing immersion from objectives, by Olympus
- Cleaning optical components, according to Leica
- Microscope cleaning and maintenance, according to Zeiss
COMPANY RECOMMENDED MICROSCOPE SANITIZING ROUTINES
- Leica how-to-sanitize-a-microscope
- Nikon recommended microscope disinfecting procedures
- Olympus: how to clean & sterilize your microscope
- Zeiss: microscope virology application disinfection routing
IMAGING TECHNOLOGIES – background information and application noted
- Widefield: by Zeiss
- Confocal: by Thorlabs
- Spinning disk: SD by Zeiss| SD by Photometrics
- Multi photon 1: (Thorlabs) | deep tissue application (Leica)
- TIRF: (MicroscopyU)
- Light sheet: (Photometrics) / open spim
- Atomic Force Microscopy: (Bruker)
- Cytometry: (BD bioscience)
- Enhanced/super resolution (Photometrics):
- Airyscan / Airyscan2: (Nature application note)
- SRRF (Andor)
- SORA
- SIM
- SMLM (PALM / STORM)
- STED/Minflux
QUANTITATIVE BIOIMAGING APPLICATIONS – background information and application notes
- FLIM
- FLIM applications and introduction (PicoQuant)
- FALCON applications and introduction (nat. Res. – Leica)
- FLIMj: an open-source ImageJ toolkit for fluorescence lifetime image data analysis. just released in bioarchive; github and ImageJ.
- FRET
- RICS
FLUOROPHORE INFORMATION:
- Fluorescence SpectraViewer (Thermofisher)
- FP-BASE
MOBILE APPLICATIONS:
- Fluorescence SpectraViewer App (Invitrogen): Apple
- Fluorescence Spectra Analyzer ( BioLegend Inc.): Android
- Huygens Nyquist calculator App (SVI) Apple | Android
- Koehler Tutor App: Koehler Illumination ((Andrew Barlow): Apple | Android
- Resolution App: Objective Lens Information (Andrew Barlow): Apple | Android
IMAGE ANALYSIS
IMAGE ANALYSIS – ONLINE SEMINARS
- NEUBIAS Academy @Home: online events targeting Bioimage Analysis Technology
http://eubias.org/NEUBIAS/training-schools/neubias-academy-home/ - SVI Huygens (deconvolution): online tutorial video series
- iBiology Online seminar series: iBiology image analysis series
- Imaris Learning Center
- AIVIA free analysis clinic’ (30 min sessions) – website
- Machine learning: Kaggle
ONLINE IMAGE ANALYSIS COURSES:
- Online image analysis course (EPFL): Image Processing and Analysis for Life Scientists
FREE IMAGE ANALYSIS TOOLS: several companies provide tools fro free, so you can be productive
- AIVIA Aivia Community freeware
- Imaris viewer free viewer download (BIF has 8 full floating)
- Leica LAS X Core free viewer download
- SVI Huygens request free 30 day trail license (BIF has 2 floating)
- Volocity offers free licenses : email to volocity@quorumtechnologies.com to request instructions (available for ±4 weeks)
- Zeiss ZEN free lite download (full license available on selected workstations)
HARDWARE CONTROL:
- Labview National Instruments training courses are available for free until at least April 30 – webpage
- μManager Open Source Microscopy Software – webpage & screencasts
- Metamoph website | knowledge base
IOF RESOURCES:
- [15-03-2020]: Image analysis software sub-page, lists the software the we have on campus
- [15-03-2020]: IOF deconvolution resource sub-page, lists several options for digital image restoration
- [15-03-2020]: IOF machine learning application sub-page, resources and applications notes
- [25-03-2020]: IOF tissue clearing assays sub-page, resources and applications notes
- [15-03-2020]: IOF microscopy course sub-page, our slides from the course from autumn 2020
- [13-06-2019]: Brief intro to imageJ macro: presentation