Light Microscopy
Light Microscopy
Light Microscopy (LMRG)
Mission
Our goal is to promote scientific exchange between researchers, specifically those in core facilities in order to increase our general knowledge and experience. We seek to provide a forum for multi-site experiments exploring “standards” for the field of light microscopy.
- Benjamin Abrams - University of California Santa Cruz
- Constadina Arvanitis - Northwestern University
- Richard Cole (Co-Chair) - Wadsworth Center, New York State Department of Health
- Natalia Dworak - University of Virginia
- Joseph Dragavon - University of Colorado
- Corinne Esquibel - Van Andel Institute
- Kari Herrington - University of California, San Francisco
- Danielle Hunt, Wadsworth Center, New York State Department of Health
- Michelle Itano - University of North Carolina
- Justine Kigenyi (EB liaison) - Kansas University Medical Center
- Soyeon Kim - University of California, San Francisco
- Kristopher Kubow - James Madison University
- DeLaine Larsen - University of California, San Francisco
- Arvydas Matiukas - SUNY Upstate Medical University
- Valeria Mezzano, NYU School of Medicine
- Thomas Pengo - University of Minnesota
- Josh Rappoport - Boston College
- Mark Sanders - University of Minnesota
- Jian Wei Tay - University of Colorado
- Erika Wee (Co-Chair) - Cold Spring Harbor Laboratory
2025
- November 2025
Image analysis basics: Understanding Image Processing (presentation) (recording) (summary) - October 2025
Managing Microscopy Data, Connecting Resources for Large Image Data, Image Data Storage, (recording) (summary) - September 2025
Understanding What Your Images Can Tell You: How to optimize for quantitative analysis (presentation) (recording) (summary) - July 2025
Scientific Image Ethics: hazards on the road from Photoshop to AI (recording) ( summary) (presentation) (attached – link to web page) - June 2025
Machine Learning Cell Segmentation in ImarisAI and Imaris (recording) (summary) - May 2025
Fiji plus introduction (recording) (summary)
2024
- December 2024
Commercial AI Tools (summary)- Andrea Papaleo, PIXIMI
- Peter Bankhead, QuPath,
- Here are the links that have all the latest QuPath-related information:
- https://qupath.github.io - the main software (release candidates for v0.6.0 are there, final release early next year)
- https://qupath.readthedocs.io/ - the documentation, including step-by-step tutorials
- https://www.youtube.com/c/qupath - YouTube channel, with talks & more tutorials
- https://forum.image.sc/tag/qupath - discussion forum
- November 11, 2024
Commercial AI Tools (summary)- Kevin O’Keefe Ph.D., ZEISS (arivis)
- Fabian Svara, Ariadne.ai
- October 8, 2024
Commercial AI Tools (summary)- George Glekas, Evident Scientific
- Tomas Silva Santisteban, Imaris
- Joseph DiPietro, Nikon
- September 10, 2024
Commercial AI Tools (summary)
Presentations:- Daniel Miranda, LeicaMicrosystems (Aivia)
- Nick Beavers, Media Cybernetics
- Philipp Kainz, Kolaido
- July 30, 2024
Applications of AI for Image Analysis - June 18, 2024
AI for Image Acquisition - May 21, 2024
Introduction to AI for Microscopy - March 12, 2024
Focus on Chat Bots (Prework) and (Presentation) - February 21, 2024
Town Hall – Focus on AI in Imaging Core Facilities
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ABCD series (October – December)
ABRF Bioimaging Community Discussions (ABCD)
Upcoming Schedule (October – December 2025)
Register here
The ABRF Bioimaging Community Discussions (ABCD) continue in October with a series of programs to review currently available commercial AI tools and a pair of “open discussion” sessions for attendees to share their frequently asked questions (FAQ) and discuss potential follow-up programming, including at ABRF meetings next year.
You can choose to register for any of all these events at the link above.
These sessions will be facilitated by members of the ABRF Light Microscopy Research Group (LMRG) with other speakers included for select sessions. To encourage open and candid conversations, these sessions will not be recorded, however, a summary along with any materials presented, will be posted to the ABRF web site.
We hope to see you at a future program. Contact us if you have suggestions for future topics.
AI in Imaging Core Facilities (list in reverse chronological order):
- February 21 – Town Hall – Focus on AI in Imaging Core Facilities
- March 12 – Focus on Chat Bots (Prework) and (Presentation)
- May 21 – Introduction to AI for Microscopy
- June 18 – AI for Image Acquisition
- July 30 – Applications of AI for Image Analysis
- September 10 – Commercial AI Tools - add links from Workshop/Webinars page
(summary and 3 presentations)
3D Image Analysis Tools and Reproducibility Event
Wednesday, April 27, 2022
Workshop breakout session recordings:
Nearly 100 attendees participated in this session on 3D image analysis tools and how they can help improve reproducibility, hosted by the Light Microscopy Research Group.
This event was centered around the LMRG’s ongoing study of reproducibility in 3D image analysis in which we seek to characterize and identify sources of (ir)reproducibility in 3D segmentation. Representatives from several major 3D analysis platforms walked attendees through how to segment and analyze the images from our study and discussed how their platforms support reproducible image analysis.
This program was targeted to people who are interested in learning more about a specific image analysis platform, learning how to use an image analysis tool better, and/or learning about how reproducibility is addressed by these platforms.
If you have questions about the LMRG study, please contact LMRG member Jessica Hornick for more information.
New LMRG Study - Volunteers Needed!
The Light Microscopy Research Group of the ABRF is launching a study to assess reproducibility in quantitative image analysis and needs YOUR help! We are seeking volunteers to segment 3D fluorescence microscope image sets and provide us with both their analysis and their analysis strategy. Our goal is not to find novel segmentation algorithms, but to compare segmentation results and strategies across a broad cross-section of volunteer analysts.
You can help by analyzing one (or more!) images for us! We need participants from all levels of image analysis experience. Everyone can participate - from students to core directors to image analysis experts. See our study website to find-out more: https://sites.google.com/view/lmrg-image-analysis-study
November 2020 ABRF LMRG/Industry Partner Discussion
The Light Microscopy Research Group and Corporate Relations Committee organized a conversation between light microscopy user groups and corporate partners, including Leica, Nikon, Olympus and Zeiss. This conversation provided an opportunity for each company to explain how they are being impacted by the COVID-19 pandemic and how they are adapting to the evolving needs of their customers.
Date: 11/18/2020
Time: 1:00-2:30 EST
View session recording.
Participants:
Ben Abrams, ABRF Light Microscopy Research Group and Corporate Relations Committee member, Director - Life Science Microscopy Facility Univ. of California Santa Cruz
Rich Cole, ABRF 2020 President, Light Microscopy Research Group member, Director - Advanced Light Microscopy & Image Analysis Core, New York State Dept. of Health Wadsworth Center
Joshua Rappoport, ABRF Light Microscopy Research Group member, Executive Director - Research Infrastructure at Boston College, Secretary – Core Technologies for Life Sciences
Michelle Itano, Director, UNC Neuroscience Microscopy Core Facility
Leica:
Greg Eppink General Manager Microscopy
Ryan Hrejsa, Senior Marketing Manager
Nikon:
Mike Gallo, General Manager, Service
Mike Johnson, Senior Regional Manager, Sales
Lynne Chang, Senior Marketing Manager
Olympus:
Shane Andrews, Manager, Sales Research Market, Life Science, Olympus Corporation of the Americas Scientific Solutions Group
Kerry Israel, Manager, Marketing Communications, Life Science, Olympus Corporation of the Americas Scientific Solutions Group
Zeiss:
Joseph Huff, Head of Marketing, North America, Zeiss Research Microscopy Solutions
Rosey Manser, Head of Business Development for Core Facilities
Studies
Activities
| 1) | ABRF2014 LMRG Group and CCMA Travel Award Winners - Richard Cole, John Russ, and Claire Brown (2,464K) - CCMA Travel Award Winners (1,934K) |
| 2) | ABRF2013 LMRG Photo - ABRF2013 LMRG Photo |
| 3) | ABRF 12 RG group photo - 2012 Meeting Group Photo |
| 4) | ABRF 12 RG intro talk - LMRG 2012 Overview Talk |
| 5) | ABRF 12 RG data talk - Study #2 Presentation (7,190K) |
| 6) | Proteomics workshop-- Get on Your Way to Microproteomics with laser Microdissection - Proteomics - Sarah Baxter |
| 7) | Proteomics workshop-- Sample prep - Tissue Proteomics Sample Preparation Leica Talk |
| 8) | ABRF 11 LMRG group photo - View Document (3,315K) |
| 9) | ABRF 11 RG talk - View Document (13,284K) |
| 10) | ABRF 2010 talk - View Document (4,643K) |
| 11) | Talk for ABRF 09 - View Document (10,567K) |
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Microsc and Microanal. 2013 Dec;19(6):1653-68.Cole, RW, Thibault, M, Bayles, CJ, Eason, B, Girard, AM, Jinadasa, T, Opansky, C, Schulz, K, Brown, CM,
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Microsc Microanal. 2011 Aug;17(4):598-606.Stack RF, Bayles CJ, Girard AM, Martin K, Opansky C, Schulz K, Cole RW.Microsc Microanal.
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Nature Protocols 6 (2011):1929RW Cole, T Jinadasa, CM Brown
Presentations
- ABRF Bioimaging Community Discussion
June 2025 (recording) (summary) - ABRF Bioimaging Community Discussion
May 2025 (recording) (summary)
Protocols
| 1) | This is a paper written by Cole and Brown and gives a lot of background on how to measure point spread functions, why you may want to measure them, how to prepare bead slides and then a detailed protocol for setting up the instrument and measuring and interpreting the PSF. This article should be looked at first before referring to the specific protocols for the individual microscope platforms. - Nature Protocols Paper (1,371K) |
| 2) | PSF Protocol Leica SP5 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Leica SP5 |
| 3) | PSF Protocol Nikon A1 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Nikon A1 |
| 4) | PSF Protocol Olympus FV1000 - Measuring the PSF with the 0.175 um green fluorescent bead sample. - PSF Protocol Olympus FV1000 |
| 5) | PSF Protocol Zeiss 510 - Measuring the PSF with the 0.175 um green fluorescent bead sample using the AIM software. - PSF Protocol Zeiss 510 |
| 6) | Spectral Accuracy Protocol Leica SP5 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. - Spectral Accuracy Protocol Leica SP5 |
| 7) | Spectral Accuracy Protocol Olympus FV1000 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. - Spectral Accuracy Protocol Olympus FV1000 |
| 8) | Spectral Accuracy Protocol Zeiss 710 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. Uses the ZEN software. - Spectral Accuracy Protocol Zeiss 710 (261K) |
| 9) | Spectral Accuracy Protocol Zeiss 510 - A mirror slide will be provided and you will look at the reflections of the laser lines into the spectral detector to determine if the wavelength readouts are accurate. Uses the AIM software. - Spectral Accuracy Protocol Zeiss 510 |
| 10) | Spectral Separation Accuracy Protocol Leica SP5 - Protocol for spectral separation testing of software un-mixing with double orange stained beads. - Spectral Separation Accuracy Protocol Leica SP5 - Bead Core Spectra Text File - Bead Ring Spectra Text File - Bead Core Spectra lsf File (12K) - Bead Ring Spectra lsf File (9K) |
| 11) | Protocol for testing the spectral separation accuracy of the Olympus FV1000. - Spectral Separation Protocol Olympus FV1000 (1,133K) |
| 12) | Study #1 Laser Stability, Alignment and Co-registration Protocol - Study #1 Laser Stability, Alignment and Co-registr |
| 13) | Improved GFP imaging in live cells - Improved GFP imaging in live cells |
Publications
- Stack, R., Bayles, C., Girard, A., Martin, K., Opansky, C., Schulz, K., Cole, and R.W. (2011) Quality Assurance Testing for Modern Optical Imaging Systems”. Microsc Microanal. 17(4): 598-606. DOI: 10.1017/S1431927611000237. PMID: 21477410
- Cole, R.W., Jinadasa, T., Brown, C.M. (2011) “Measuring and Interpreting Point Spread Functions to Determine Confocal Microscope Resolution and Ensure Quality Control”. Nat Protoc. 6(12): 1929-1941. DOI: 10.1038/nprot.2011.407. PMID: 22082987
- Cole, R.W., Thibault, M., Bayles, C., Eason, B., Girard, A., Jinadasa, T., Opansky, C., Schulz, K., Brown, C. (2013) “International Test Results for Objective Lens Quality, Resolution, Spectral Accuracy and Spectral Separation for Confocal Laser Scanning Microscopes (CLSM)”. Microsc Microanal. 19(6): 1653-1668. DOI: 10.1017/S1431927613013470. PMID: 24103552
- Brown, C., Reilly, A., Cole, R.W. (2015) “A Quantitative Measure of Field Illumination”. J Biomol Tech. PMID: 25802488
- Adrams, B. et. Al. (2023) Tissue-Like 3D Standard and Protocols for Microscope Quality Management in Microscopy and Microanalysis. doi: https://doi.org/10.1101/2022.08.14.503777
- Pengo, T, et. Al. (2024) Comparison of independent analyses of identical image sets reveals significant analyst-to-analyst variability. In press
| Member Name | Organization | Details |
|---|---|---|
| Pamela Scott Adams | Trudeau Institute | Ad hocEB Liaison: 02/09 - 03/10 |
| Carol J Bayles | Cornell University | Member: 04/08 - 05/15 |
| Claire M Brown | McGill University | Chair: 03/11 - 04/15 Member: 09/10 - 03/18 |
| Lisa Cameron | Duke University | Member |
| Richard Cole | Wadsworth Center | Chair: 03/08 - 03/11 |
| Arnold M. Falick | HHMI-UC Berkeley | Ad hocEB Liaison: 03/08 - 02/09 |
| Paul Furcinitti | UMass Medical School | Member: 05/13 - 12/14 |
| Anne-Marie Girard | Center for Genome Research and Biocomputing, Oregon State University | Member: 02/10 - 05/15 |
| William G Hendrickson | Univ. of Illinois, Chicago | EB Liaison: 09/13 - 04/14 |
| Jessica Hornick | Northwestern University | Member through 12/22 |
| Karen R Jonscher | University of Colorado Denver | Ad hocEB: 04/10 - 03/13 |
| Gary Laevsky | Princeton University | Member: 01/17-04/19 |
| Karen Martin | West Virginia University | Member: 12/08 - 05/15 |
| George McNamara | U Miami | Member: 06/11 - 03/13 Ad hoc: 03/13 - 12/14 |
| Kary Oakleaf | Molecular Probes, Life Technologies | Member: 06/13 - 12/14 |
| Cynthia Opansky | Blood Center of Wisconsin | Member: 02/09 - 12/13 |
| James Powers | Indiana University | Member through 12/22 |
| Joshua Rappoport | Northwestern University | Member: 03/15-01/19 |
| Katherine Schulz | Blood Center of Wisconsin | Member: 03/09 - 04/13 |
| Robert F. Stack | Wadsworth Center NYSDOH | Member: 02/09 - 03/11 |
| Marc Thibault | Ecole Polytechnique | Member: 06/11 - 03/14 |
| Erika Wee | McGill University | Chair: 04/15 - 05/18 |
| Frances Weis-Garcia | Memorial Sloan Kettering Cancer Center | EB Liaison: 05/14 - 04/15 |
| Linda Callahan | University of Rochester Medical Center | (through 2023) |
| Guillermo Marques | University of Minnesota | (through 2023) |
Questions or interest in joining an ABRF research group? Contact us!