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Integrated Light Microscopy: The Integrated Light Microscopy Facility (ILMF) functions as a supervised, user-based Core providing state-of-the-art microscopy imaging capabilities to all University investigators. The primary mission of the Facility is to provide a valuable, unique service to the University community by furnishing high-quality microscopy instrumentation, user training, image analysis tools, and expert assistance. The ILMF is directed by Dr. Benjamin Glick and managed by three full-time technical directors. Together Dr. Christine Labno, Dr. Lorraine Horwitz, and Mr. Khalil Rodriguez provide specialized expertise in superresolution and sub-diffraction imaging, live cell imaging, expansion microscopy and tissue clearing methods, and higher order multiplex immunostaining (including antibody generation and testing) as well as extensive experience in image processing and analysis. The main location is a custom-designed space in the Knapp Center for Biomedical Discovery (KCBD) room 1250. The facility houses 18 microscopes, including four with superresolution capability (the Leica Ground State Depletion / TIRF microscope, the 3i Lattice Lightsheet, the Leica SP8 3D STED-3X white-light laser spectral confocal, and Super-resolution through Optical Reassignment (SoRa) 3i Marianas spinning disc confocal. Other systems include a Leica Stellaris8 Falcon with white light laser and fluorescence lifetime imaging, two additional spinning disk confocal systems, a stereomicroscope, a CaliberID upright large format confocal microscope, a La Vision Ultra II cleared sample lightsheet, two brightfield and full fluorescence widefield microscopes (the Zeiss Axio Observer with the AI sample finder feature and an Olympus IX81), and an Axioskop histology microscope. The facility can accommodate live cell imaging in multiple formats, including the 3i Lattice Lightsheet system, seven other systems with full-wrap incubation chambers (three with CO2) and two stage-top incubation systems. Three high-resolution digital slide scanners are operated as a drop-off service. These scanners yield digital slides containing detailed color histology and multi-color fluorescence images. The facility offers high-end analysis software (ImageJ/Fiji, QuPath, OlyVia, Zeiss Zen Blue, LAS X, Arivis Vision4D, Imaris, and Huygens Pro), free temporary networked data storage, and dedicated workstations for data analyses and presentation (including virtual reality). Details and policies can be found on the Core website. https://voices.uchicago.edu/confocal/
Acknowledgment:
[Technique/technology] was performed in the Integrated Light Microscopy Core at University of Chicago, which receives financial support from the Cancer Center Support Grant (2P30CA014599). RRID: SCR_019197
We thank The University of Chicago Integrated Light Microscopy Core, especially [staff name], for their assistance with [technique/technology]. RRID: SCR_019197
Integrated Light Microscopy Core RRID: SCR_019197
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Here are sample sentences that anyone using the Facility can add to the Acknowledgements or Materials and Methods sections of publications. Resources are in alphabetical order.
Acknowledging the Facility or the Technical Directors and listing the Core equipment you used in the Materials and Methods section helps us demonstrate how much our Core contributes to the University community and track the impact of each piece of equipment on research infrastructure.
General Facility Acknowledgement: Imaging (and/or image processing and/or data analysis) was performed at the University of Chicago Integrated Light Microscopy Core RRID: SCR_019197.
You may also acknowledge special contributions to imaging or image analysis by Dr. Loraine Horwitz, Dr. Christine Labno or Mr. Khalil Rodriguez if you wish.
Arivis software: Image processing was performed using Arivis Vision4D software v. 3.1 (arivis AG, Rostok, Germany).
Axio Observer 7 in KCBD 1250F: Images were captured with a Zeiss Axio Observer 7 inverted widefield microscope with Zeiss Axiocam 705 monochrome and Axiocam 305 color CMOS cameras run by Zeiss Zen Blue (Carl Zeiss Microscopy, Thronwood, NY).
Axioskop in KCBD 1250A: Images were captured with a Zeiss Axioskop upright microscope with a Zeiss Axiocam color CCD camera (Carl Zeiss Microscopy, Thornwood, NY) run by the QCapture suite (QImaging, Surry, BC).
Axiovert 200m in KCBD 1250F (retired): Images were captured with a Zeiss Axiovert 200m inverted epifluorescence microscope (Carl Zeiss Microscopy, Thornwood, NY) with (CHOOSE ONE) a Hamamatsu Flash 4.0 camera (Hamamatsu Photonics, Skokie, IL) for fluorescence imaging OR a Zeiss Axiocam digital color CCD camera (Carl Zeiss Microscopy, Thornwood, NY) for histology imaging run by SlideBook software (Intelligent Imaging Innovations, Denver, CO).
Imaris software: Image processing was performed using Bitplane Imaris software v. 9.1.2 (Andor Technology PLC, Belfast, N. Ireland).
Lattice Lightsheet in KCBD 1250B: Images were captured with a 3i Lattice Lightsheet microscope with Bessel Beam Illumination (Intelligent Imaging Innovations, Denver, CO) with dual Hamamatsu Orca Fusion BT cameras (Hamamatsu Photonics, Skokie, IL) run by Slidebook software (Intelligent Imaging Innovations, Denver, CO).
LaVision Ultramicroscope II in KCBD 1250C: Lightsheet Images were captured with a LaVision BioTec UltraMicroscope II (Miltenyi Biotec, Bergish Gladbach, Germany) run by ImSpector Pro v. 7_124 software (LaVision BioTec, Bielefeld, Germany).
Leica GSD in KCBD 1250C: Images were captured with a Leica SR GSD 3D / 4 color TIRFM fluorescence microscope (Leica Microsystems, Inc., Buffalo Grove, IL) with an Andor iXon Ultra EM-CCD camera (Andor Technology PLC, Belfast, N. Ireland).
Leica SP5 2-photon in KCBD 1250B: Images were captured with a Leica SP5 Tandem Scanner Spectral 2-photon confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL).
Leica STED-SP5 in KCBD 1250F: Images were captured with a Leica TCS SP5 II STED laser scanning confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL). This instrument was purchased with funds obtained through NIH S10 OD010649 granted to Dr. Gopal Thinakaran and Dr. Vytas Bindokas in 2012.
Leica SP8 3D STED in KCBD 1250G: Images were captured with a Leica SP8 3-color 3D STED laser scanning confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL).
Leica Stellaris 8 in KCBD 1250G: Images were captured with a Leica Stellaris8 laser scanning confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL).
Marianas in KCBD 1250F: Images were captured with a 3i Marianas Yokogawa-type spinning disk confocal microscope with Evolve EM-CCD camera (Photometrics, Tucson, AZ) running SlideBook software (Intelligent Imaging Innovations, Denver, CO). This instrument was purchased with funds from NIH S10 RR028898 granted to Dr. Jerrold Turner and Dr. Vytas Bindokas in 2010.
Olympus “live cell” DSU Spinning Disk in KCBD 1250F: Images were captured with an Olympus DSU spinning disk confocal microscope (Olympus Corporation of the Americas, Center Valley, PA) with a Hamamatsu model C9100 EM-CCD camera (Hamamatsu Photonics, Skokie, IL) run by SlideBook software (Intelligent Imaging Innovations, Denver, CO).
Olympus IX81 widefield in KCBD 1250C: Images were captured with an Olympus IX81 inverted epiflurorescence microscope with the Olympus Zero Drift Correction auto re-focusing system (Olympus Corporation of the Americas, Center Valley, PA) with a Hamamatsu Orca Flash 4.0 sCMOS camera (Hamamatsu Photonics, Skokie, IL) run by Slidebook software (Intelligent Imaging Innovations, Denver, CO).
SoRa Marianas in KCBD 1250F: Images were captured with a 3i Marianas Super-resolution through Optical Reassignment (SoRa) Yokogawa-type spinning disk confocal microscope (Intelligent Imaging Innovations, Denver, CO) with dual Prime 95B Illuminated Scientific CMOS (Teledyne Photometrics Vision Solutions, Tucson, AZ) run by Slidebook software (Intelligent Imaging Innovations, Denver, CO).
Stereomicroscope in KCBD 1250C: Images were captured with an Olympus SZX-Zb12 Research Stereomicroscope (Olympus Corporation of the Americas, Center Valley, PA) with a QIMaging Retiga-EXi FAST camera (QImaging, Surrey, BC) run by Slidebook software (Intelligent Imaging Innovations, Denver, CO).
Whole Slide Scanner CRi 20x in KCBD 1250D: Digital image files were created with a 3D Histech Pannoramic MIDI whole slide scanner (Epredia, Kalamazoo, MI) with a Zeiss AxioCam MRm CCD camera (Carl Zeiss Microscopy, Thornwood, NY). Individual images were created with the 3D Histech Pannoramic Viewer software ((3DHistech Kft, Budapest, Hungary).
Whole Slide Scanner Olympus VS200 in KCBD 1250E: Digital image files were created with an Olympus VS200 Research Slide Scanner (Olympus / Evident, Center Valley, PA) with a Hamamatsu ORca-Fusion camera (Hamamatsu Photonics, Skokie, IL). Individual images were created with the OlyVIA Viewer software (Olympus / Evident, Center Valley, PA).