Integrated Light Microscopy Core

Boilerplate Language for Grants

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. Vytas Bindokas, Dr. Christine Labno and Ms. Shirley Bond have a combined 70 years of microscopy experience with specialties in live cell imaging, physiologic measurements, clinical immunopathology, and 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, and houses 14 microscopes, including four with superresolution capability (the Leica Ground State Depletion superresolution/TIRF microscope, lattice Lightsheet, the Leica SP5 II STED-CW superresolution confocal, and Leica SP8 3D STED-3X white-light laser spectral confocal). Other systems in the KCBD location include a NEW Leica Stellaris8 WLL Falcon WLL confocal system, two Olympus DSU spinning disk confocal systems, a stereomicroscope, CaliberID upright scanning confocal microscope, a La Vision ultra II cleared sample lightsheet microscope, and two brightfield and fluorescence light microscopes. The facility can accommodate live cell imaging in multiple formats, including the Zeiss Lightsheet Z1 SPIM system, the 3-I Lattice Lightsheet system, the Olympus VivaView incubator microscope, three systems with full-wrap incubation chambers (two with CO2) and three stage-top incubation systems. Two high-resolution digital slide scanners are operated as a drop-off service. These scanners yield digital slides containing detail equivalent up to 80x magnification for color histology and multi-color fluorescence materials. The Abbott 129 satellite location houses three microscopes including a Leica SP5 2-photon laser scanning confocal, a 3-I Marianas laser spinning disk confocal, and an Axiovert 135 fluorescence/DIC microscope. The facility offers high-end analysis software (MetaMorph, Arivis Vision4D, Imaris, Huygens Pro, ImageJ, etc), free temporary networked data storage, and workstations (two are very high-end computation and graphics capable) for data analyses and presentation (including virtual reality). Details and policies can be found on the Core website.

Boilerplate Language for Publications

All of the following information is also available as a Word doc

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 Facility. You may also acknowledge special contributions to imaging or image analysis by Ms. Shirley Bond, Dr. Vytas Bindokas, and/or Dr. Christine Labno if you wish.

Arivis software: Image processing was performed using Arivis Vision4D software v. 3.1 (arivis AG, Rostok, Germany).

Axioskop in KCBD 1250C: Images were captured with a Zeiss Axioplan upright microscope with a Zeiss Axiocam color CCD camera (Carl Zeiss Microscopy, Thornwood, NY) run by the QCapture suite (QImaging, Surry, BC).

Axiovert 100 in KCBD 1250F (retired in 2017): Images were captured with a Zeiss Axiovert 100TV inverted epifluorescence microscope (Carl Zeiss Microscopy, Thornwood, NY) with a Retiga EXi CCD camera (QImaging, Surry, BC) run by SlideBook 5.5 software (Intelligent Imaging Innovations, Denver, CO).

Axiovert 135 in Abbott 129: Images were captured with a Zeiss Axiovert 135 inverted epifluroescence microscope (Carl Zeiss Microscopy, Thornwood, NY) with a MicroMax camera (Roper Scientific, Trenton, NJ) run by Micro-Manager software (laboratory of Dr. Ron Vale, University of California San Francisco, San Francisco, CA).

Axiovert 200m in KCBD 1250F: 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 6.0 software (Intelligent Imaging Innovations, Denver, CO).

Fluoview 1000 in KCBD 1250B (retired in 2020): Images were captured with an Olympus Fluoview 1000 laser scanning confocal microscope with Olympus Image Capture software (Olympus Corporation of the Americas, Center Valley, PA). Huygens Deconvolution software: Images were deconvolved with Huygens Pro software v. 4.3 (Scientific Volume Imaging, Hilversum, The Netherlands).

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 a Hamamatsu Orca Fusion camera (Hamamatsu Photonics, Skokie, IL) run by Slidebook software (Intelligent Imaging Innovations, Denver, CO).

LaVision Ultramicroscope II: 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 1250B: 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 Abbott 129: 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 1250G: Images were captured with a Leica TCS SP5 II STED laser scanning confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL).

Leica SP8 3D STED in KCBD 1250G: Images were captured with a Leica SP8 3D STED laser scanning confocal microscope (Leica Microsystems, Inc., Buffalo Grove, IL). Leitz in Abbott 129: Images were captured with a Leitz Diaplan inverted epifluroescence microscope (Leica Microsystems, Buffalo Grove, IL) with a QImaging MicroPublisher 3.3 CCD camera and QCapture suite software (QImaging, Surrey, BC).

Lightsheet Z.1 in KCBD 1250C: Images were captured with a Zeiss Lightsheet Z.1 Selective Plane Illumination microscope (Carl Zeiss Microscopy, Thornwood, NY) with tandem PCO.edge sCMOS cameras (PCO.Imaging, Kelheim, Germany) and Zeiss Zen imaging software. Marianas in Abbott 129: Images were captured with a 3i Marianas Yokogawa-type spinning disk confocal microscope with an Evolve EM-CCD camera (Photometrics, Tucson, AZ) running SlideBook v6.0 software (Intelligent Imaging Innovations, Denver, CO).

Olympus “fixed sample” 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 an Evolve EM-CCD camera (Photometrics, Tucson, AZ) run by SlideBook v6.0 software (Intelligent Imaging Innovations, Denver, CO).

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 v6.0 software (Intelligent Imaging Innovations, Denver, CO).

Olympus IX81 (was TIRF) microscope in KCBD 1250F: 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 6.0 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 40x histology: Digital image files were created with a 3D Histech Pannoramic SCAN whole slide scanner (Epredia, Kalamazoo, MI) with a Stingray F146C color camera (Allied Vision Technologies, Stadtroda, Germany). Individual images were created with the 3D Histech Pannoramic Viewer software (3DHistech Kft, Budapest, Hungary).

Whole Slide Scanner 20x fluorescent: 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).

VivaView incubator microscope in KCBD 1250B: Images were captured with an Olympus VivaView incubator-based, epifluorescence microscope (Olympus Corporation of the Americas, Center Valley, PA) run by MetaMorph software (Molecular Devices LLC, Sunnyvale, CA).