Summary of CAM and NIC activities in Spring and Summer 2023
The Center for Advanced Microscopy (CAM) and the Nikon Imaging Center (NIC) is committed to outreach, career development, and capacity-building. During the Summer of 2023, CAM/NIC together with Greg Schwartz, PhD and Felix Nunez, PhD hosted the PairUP workshop, whereby 18 African American scientists from across the USA joined us for training on Multiphoton Microscopy and Deep Tissue Imaging. We have also strengthened our expertise in mechanobiology methods, as well as deep learning for image analysis. CAM and NIC has also been represented in various national and international meetings. We continue to collaborate with international organizations such as Bioimaging North America and Latin American Bioimaging in multiple projects. We also share several achievements of CAM and NIC, and announce upcoming courses, workshops, and new instruments soon becoming part of our facility. We aim to provide state-of-the-art imaging technology, and our doors are always open.
Good News From CAM
David Kirchenbüchler, PhD, Appointed Research Assistant Professor
In July 2023, Dr. David Kirchenbüchler, image analyst at CAM, was appointed as Research Assistant Professor of Cell and Developmental Biology. Congratulations David! We celebrate this great achievement.
CAM and Collaborators in Ecuador and Bolivia Awarded Company of Biologists Grant: 'Democratizing Microscopy'
CAM, together with collaborators in Ecuador and Bolivia, was awarded a highly competitive Company of Biologists grant to host the workshop "Democratizing Microscopy in Latin America: Imaging Across Scales and Regions."
Image by Nicolas Piguel, PhD, postdoctoral fellow, Peter Penzes Lab.
What's New?
MolDev ImageXpress is operational
The ImageXpress high-throughput confocal microscope is now fully operational, including liquid handling. This will enable high-throughput, long-term imaging with the possibility of automated compound delivery/removal.
Several workstations will be equipped with the relevant software for image analysis. If you are interested in a consultation or in receiving training for this instrument, feel free to reach out to Mariana De Niz at mariana.denizhidalgo@northwestern.edu
Leica EM ACE600 Sputter Coater is operational
The newly acquired Leica EM ACE600 Sputter Coater is now operational. This equipment is state-of-the-art for glow discharge, platinum replicas, platinum and carbon coating. If you are interested in learning more about this instrument, contact Lennell Reynolds, Jr., at l-reyjr@northwestern.edu or Farida Korobova at farida.korobova@northwestern.edu
New computer workstation is operational
The newly acquired workstation is now operational. This computer is equipped with the latest software and hardware for optimized designs for deconvolution workflows using Nikon Elements and training deep neural networks. If you are interested in using this equipment, contact David Kirchenbüchler at david.kirchenbuchler@northwestern.edu
Image by Dileep Varma, PhD, Assistant Professor of Cell & Developmental Biology
Growing Expertise at CAM and NIC
Mechanobiology and Atomic Force Microscopy
CAM staff have great expertise in atomic force microscopy (AFM) applied to static and dynamic measurements, and we are constantly expanding the types of experiments we support.
During the spring and summer of 2023, Peter Dluhy, David Kirchenbüchler and Mariana De Niz have been increasing their skillsets related to AFM.
With our growing expertise in the field of AFM, we are happy to offer improved service to CAM and NIC users. If you are interested in incorporating AFM on your research projects, please reach out to Peter Dluhy at peter.dluhy@northwestern.edu, David Kirchenbüchler at david.kirchenbuchler@northwestern.edu, or Mariana De Niz at mariana.denizhidalgo@northwestern.edu
Deep Learning and the Bioimage Archive
CAM staff is able to support a wide range of projects requiring image analysis. We are constantly expanding our expertise in this rapidly-growing field. During the spring and summer of 2023, Mariana De Niz has trained on deep-learning methods for fluorescence and advanced volumetric electron microscopy data analysis, as well as napari plugins, cloud computing and the Bioimage Archive.
We are happy to offer these services to interested users. If you wish to implement these methods or discuss further details, feel free to contact Mariana De Niz mariana.denizhidalgo@northwestern.edu, David Kirchenbüchler david.kirchenbuchler@northwestern.edu or Dina Arvanitis c-arvanitis@northwestern.edu
Image by Maureen Haynes, PhD candidate, William Muller Lab.
Instruments Coming Soon
SoRa (Nikon), CAM/NIC was recently awarded an S10 grant to acquire a SoRa super-resolution confocal microscope capable of achieving 130nm resolution. It is expected to reach CAM in the Fall of 2023. We will update users when this instrument becomes operational. If you are interested in learning more about the SoRa system for your work, contact Mariana De Niz at mariana.denizhidalgo@northwestern.edu or Dina Arvanitis at c-arvanitis@northwestern.edu
Save the Date: Microscopy Courses and Seminars at CAM
Image Analysis: Fiji Introductory Course
Quarterly one-week Fiji Courses led by David Kirchenbüchler, covering basic concepts in image analysis using the open software Fiji/Image J will be offered. Click the button below to see available dates and to sign up.
Fundamentals of Microscopy: Getting the Most out of your confocal
Monthly seminar led by Dina Arvanitis, covering basic concepts in confocal microscopy on September 12 at 10:00 a.m. in the Searle Seminar Room (Lurie 1-161), Robert H. Lurie Medical Research Center.
Advanced Microscopy: Expanding CAM's Toolkit
Advanced seminar led by Mariana De Niz. Mariana joined CAM and NIC in March 2023, with a new skillset available to users including intravital microscopy, light sheet microscopy, optoacoustic imaging and optical projection tomography, mechanobiology, virtual reality, graphic design and mathematical modeling.
The seminar will take place on Monday, September 18 at 10:00 a.m. in the Searle Seminar Room (Lurie 1-161), Robert H. Lurie Medical Research Center.
CellProfiler and Ilastik Courses
Quarterly one-week CellProfiler and Ilastik course led by Mariana De Niz covering basic concepts in image analysis using two different software tools.
Upcoming dates: November 6-10, 2023. Sign up to be circulated soon.
Image by Maribel Torres-Velazquez, PhD, postdoctoral fellow, Greg Schwartz Lab.
CAM's Microscopy Courses, Seminars and Imaging Clinic
Going forward, CAM will offer monthly seminars and courses with the following structure:
- Week 1: Image analysis
- Week 2: Fundamentals of Microscopy
- Week 3 and 4: Advanced Microscopy
Preview of October Topics: Advanced Microscopy: Multiphoton Microscopy and Intravital Imaging
Advanced seminar led by Dina Arvanitis and Mariana De Niz, with invited speakers, covering multiphoton microscopy and intravital imaging. The seminar will take place in October. Watch out for our email specifying date, time and location.
Miltenyi Seminar on Tissue Clearing and Light Sheet
Invited seminar by Miltenyi speakers (makers of the LaVision light sheet), discussing tissue clearing and light sheet will take place in October. Watch out for our email specifying date, time and location.
Office Hours: Imaging Clinic
You are always welcome to contact us to schedule a time to discuss your workflow. In addition to scheduled consultations, we are opening an 'imaging clinic' in which you can drop by to get a consultation on any topic related to the microscopy workflow: experiment design, choosing fluorophores, troubleshooting, image acquisition, image analysis. Our office hours for unscheduled consultations will be Mondays from 10:00 a.m. to 11:00 a.m.
Image showing expansion microscopy, by Nicolas Piguel, PhD, postdoctoral fellow, Peter Penzes Lab.
CAM Teaching, Outreach and Community Engagement
PairUP Workshop
In June 2023, Northwestern University hosted the PairUP program for Black Imaging Scientists, focusing on the topic, "How to use multiphoton microscopy for imaging of thick biological samples." This was an event co-hosted by Dina Arvanitis, David Kirchenbüchler, Mariana De Niz, Felix Nunez, and Greg Schwartz.
We hosted 18 participants from various USA academic institutions. We are grateful for the support we received from Nikon, FSM and Office for Research to fund this event. We are very grateful for the support from various research groups (Arispe Lab, Bharat Lab, Davis Lab, Gelfand Lab, Mitchell Lab, Smith Lab and Vassar Lab) who kindly contributed samples, protocols, and helpful information that was pivotal for the success of this workshop. We are also grateful to Yesenia Navarro for her support in the organization and logistics of this event.
CAM Activities With Bioimaging North America (BINA) and Latin America Bioimaging (LABI)
Dina Arvanitis and Mariana De Niz are members of several BINA working groups including Training and Education, Communication, and Diversity, Equity and Inclusion. As part of this work they contribute, together with imaging scientists from institutions in Canada, the USA and Mexico, to develop education programs aimed at different age groups and sectors of the population; translation efforts to improve access to imaging content in different languages; outreach and communication efforts to improve accessibility to imaging-related content; and DEI programs aimed at democratizing access to microscopy. Mariana is also chair of the Outreach and Latin American integration working groups in LABI. If you are interested in learning more about the activities we do, and becoming involved, please reach out to Mariana De Niz at mariana.denizhidalgo@northwestern.edu or Dina Arvanitis at c-arvanitis@northwestern.edu
Intravital microscopy images of the gut, by Lenore Yalom, PhD student, Ronen Sumagin Lab.
Featured Images
Users of the various instruments at CAM are invited to submit their best images. Select images will be included in our newsletter and in CAM’s website gallery. Annual winners will get a 3D-printed award. Submit your high-resolution image to Mariana De Niz, mariana.denizhidalgo@northwestern.edu.
Training Opportunities
Each month, we will curate a list of training opportunities in BioImaging for interested users.
Archived Resources
(Permanent access)
- Reporting & Reproducibility in Microscopy
- Euro-Bioimaging Training Portfolio
- NEUBIAS Academy Archive
For other archived resources, check out our website.
Upcoming Training Opportunities
Listed in order of registration deadline
- Tissue Clearing Workshop at Harvard Center for Biological Imaging (to take place in January 2024)
- Analytical and Quantitative Light Microscopy at MBL, Woods Hole (to take place in Spring 2024)
- ESRIC Super-Resolution Summer School at the University of Edinburgh, Scotland (to take place in Summer 2024)
AFM Image by Peter Dluhy, confocal imaging specialist at CAM and Mariana De Niz, Research Assistant Professor and Nikon Imaging Center Manager at CAM.
Publications and new techniques
Direct Observation of the Conformational States of PIEZO1
NanoPyx: Super-Fast Bioimage Analysis Powered by Adaptive Machine Learning
Check out the new journal npj Imaging. npj Imaging is an open-access journal of the Nature publishing group, dedicated to publishing imaging research across scales and the translational pipeline.
Publications From Northwestern University and CAM & NIC Users
If you have work performed at CAM/NIC that has been recently published, please let us know, and will be happy to highlight it in our upcoming newsletter and share it with the Northwestern University and Imaging Community!
Image obtained by Mariana De Niz using samples provided by Prof. Vladimir Gelfand's Lab.
Journal Club and Outreach Programs Coming Soon
Imaging Journal Club
CAM, together with other imaging groups in Chicago, is organizing a journal club to bring together experts in the area to discuss novel microscopy-based work on a monthly basis. If you are interested in joining, please contact Mariana De Niz, mariana.denizhidalgo@northwestern.edu
Microscopy Outreach Programs
Stay tuned for upcoming CAM-led initiatives supporting microscopy for all.
Image by Manas Chakraborty, postdoctoral fellow, Dileep Varma Lab.
News From BINA
CAM and NIC have been BINA members since 2016. BINA’s mission is to engage bioimaging scientists from North America and build collaboration and partnership in the region.
BINA offers various training opportunities. Keep an eye on upcoming training events including programs organized by the lattice light sheet microscopy and expansion microscopy user groups.
Join the BINA Speaker Series
Speakers from Canada, USA and Mexico share their expertise on the use of imaging on various research topics.
BINA Image Contest
Submit your images to the BINA 2023 Image contest by October 2nd, 2023.
More Ways to Connect
Follow us on these social media channels.
- Twitter: @CAM_NUChicago
- Instagram: @microscopy.nu.cam.nic
- LinkedIn: CAM and NIC at FSM Northwestern University
- Mastodon: @CAM_NUChicago
Feel free to reach out to us if you wish to share news from your lab relevant to your imaging-based work, through our social media platforms.
Coming soon, our redesigned CAM website. Stay tuned!
Image by Enzo Bresteau, PhD, postdoctoral fellow, Brian Mitchell Lab