Microscopy Grant Services

Letters of Support:

Grant applications proposing work that will be performed by the Microscopy Service (or with their assistance) do not require letters of support unless the methods that will be used are not included in the Microscopy Service’s description in the JAX Facilities and Other Resources master document (see description below). For methods that are unusual or particularly challenging in the microscopy field, or that were recently published, please contact the Microscopy Service Associate Director to determine whether a letter of support would be appropriate.

Facilities and Other Resources Documentation:

The Microscopy Service includes standard widefield microscopy; advanced fluorescent microscopy (including confocal and spinning disk); longitudinal observation or live-cell imaging, including imaging of induced pluripotent stem cells (iPSCs) and mouse embryonic stem cells (ESCs) under various environmental conditions, including hypoxia; laser-capture microdissection; image analysis and 3D visualization; high-throughput cell-based screening; brightfield slide scanning; and automated fluorescence slide scanning. Image analysis capabilities include digital image collection, processing, quantitative analysis, and 3D visualization, which are enabled by the following software applications: Imaris 3D (Andor/Bitplane), Huygens deconvolution (SVI) via HPC access, the Leica LAS X software suite (includes the Lightning, 3D, and Leica - Analysis packages), CellProfiler™ (The Broad Institute), and Fiji/ImageJ software. The Microscopy Service also supports projects requiring use of the high-performance computing (HPC) platforms for high-content image analysis using scriptable programming languages such as ImageJ macros, and python scripts for image analysis. The Microscopy Service facilities in Bar Harbor, ME, and Farmington, CT, both include a specimen preparation area containing a CO₂ incubator and water baths, a 4°C refrigerator, a -20°C freezer, a microcentrifuge, and a small tissue-culture hood. Microscopy Service staff have extensive experience and expertise in confocal, widefield, and super-resolution microscopy methods, and are dedicated to consultation, experimental design, protocol development, sample preparation, and data acquisition and analysis, as well as instrument operation and training.  

Microscopy Service equipment located in Bar Harbor, ME

• Stellaris WLL/FALCON/Lightning super-resolution confocal microscope with variable excitation laser lines and red-shifted HyD hybrid detectors for NIR imaging; Leica

• SP8 WLL-AOBS/Lightning super-resolution confocal microscope featuring nine laser lines, including a 594-nm laser; two HyD (photon-avalanche hybrid) detectors and hardware-coupled Lightning deconvolution; and an LAS X Navigator for fast, multi-point acquisition of 3D image stacks; Leica

• Stellaris DIVE/4Tune/FALCON LIA™chroic multi-photon instrument featuring two mode-locked, green-light diode pump/pulsed lasers (Spectra-Physics^®) with 3 watts of maximum output at 800/900 nm (max wavelength for TPEM between 690–1300 nm). Pre-chirp/GDD for the Insight-X3 and high-powered, 70 fs pulse duration Maitai eHP, as well as fluorescence lifetime imaging (FLIM) using Fast-FLIM FALCON solution with Phasor analysis module; Leica
• LSM800 Airyscan confocal microscope with four lasers, providing super-resolution imaging; Zeiss
• THUNDER widefield microscopewith a fast-acquisition, four-slide scan setup with computational clearing and in-line deconvolution, a Lumencor^® 8-LED illuminator, and a 12-bit (high/low signal)/16-bit (high dynamic range) camera; Leica
• DMi8 inverted widefield microscope with LAS X Navigator slide-screening software; Leica
• Ti2 ECLIPSE widefield microscope with an Andor camera (35 fps) and an Okolab stage-top incubator for well-plate screening and live-cell imaging; Nikon
• Opera Phenix quad-camera high-content screening system for 3D 96-well-plate imaging; PerkinElmer (now Revvity)
• NanoZoomer S210 digitalslide scanners (service-operated); Hamamatsu (2)
• VS200 high-capacity fluorescence slide scanner (service-operated); Olympus
• M165FC automated stereomicroscope for large-tissue DoF imaging; Leica
• UltraMicroscope II light sheet microscope, mesoSPIM with three excitation laser lines; LaVision/Miltenyi Biotec
• Three high-performance, high-memory workstations for high-content 3D-image analysis and gpGPU (CUDA^®) processing capability for Bitplane Imaris 3D and PE Harmony image analysis
• SVI Huygens Deconvolution Software in a high-RAM/high-end GPU Computer can be accessed locally or remotely via the JAX network
• Ti-Eclipse Course Microscope educational microscope; Nikon
• JAX Image Tools (in-house development) for scalable, web-based, batchable image processing to simplify downstream image analyses
• OMERO-based image viewing and file distribution system with feasible long-term storage capacities

Microscopy Service equipment located in Farmington, CT

• Dragonfly multimodal live-cell imaging spinning disk confocal system with a fully enclosed Okolab cage incubator; Oxford Instruments Andor Ltd. 
• Inverted SP8 WLL combination instrument for super-resolution by stimulated emission depletion and digital light-sheet microscope, providing 30-nm super-resolution (STED mode) or mm-sized sample imaging (DLS mode); FALCON system provides the capability to perform fluorescence lifetime imaging (FLIM/FALCON) and fluorescence correlation microscopy (FCS) using a tunable 47–680-nm light source; adaptive, motorized optics (93x/1.3 motCORR) allow sub-diffraction limit imaging (limit = 270 nm at 525-nm emission) achieving up to 22-nm lateral resolution and imaging depths of 300 µm into cleared tissue sections; Leica
• SP8 WLL-AOBS/Lightning confocal microscope with a tunable laser for variable fluorophore excitation between 470–680-nm, and LAS X Navigator for fast, multi-point acquisition of 3D stacks; includes HyD (photon-avalanche hybrid) detectors and hardware-coupled Lightning deconvolution; Leica 
• Opera Phenix quad-camera high-content screening system for 3D 96-well-plate imaging; PerkinElmer (now Revvity)
• THUNDER widefield microscopewith a fast-acquisition, four-slide scan setup with computational clearing and in-line deconvolution, a Lumencor^® 8-LED illuminator, and a 12-bit (high/low signal)/16-bit (high dynamic range) camera; Leica
• Ti ECLIPSE inverted widefield microscope, featuring a fast monochrome sCMOS camera and an Okolab stage-top incubator supporting live-cell imaging of cells under various environmental conditions such as hypoxia; Nikon
• M165 fluorescence stereomicroscope; Leica
• Accuva Cellect Laser Capture Microdissection System (a redesign of Thermo Fisher Scientific’s Arcturus^XT™ system) features UV and IR lasers with integrated brightfield and fluorescent optics; Laxco
• NanoZoomer-SQ digital slide scanner, a desktop unit that generates whole-slide images from single slides; Hamamatsu
• Three high-performance, high-memory workstations for high-content 3D-image analysis and gpGPU (CUDA^®) capability for Bitplane Imaris 3D and PE Harmony image analysis
• SVI Huygens Deconvolution Software to remotely access a high-RAM/high-end GPU computer at the JAX Bar Harbor, ME, campus via the JAX network
• JAX Image Tools (in-house development) for scalable, web-based, batchable image processing to simplify downstream image analyses
• OMERO-based image viewing and file distribution system with feasible long-term storage capacities

Acknowledgement & Authorship:

If you have used any of JAX’s Scientific Services please remember to acknowledge the Service(s) used, in all manuscripts, publications, grant applications, press releases, and presentations.

Please remember to acknowledge the use of the JAX Microscopy Service in manuscripts and grant applications:

"We gratefully acknowledge the contribution of [optional: name of person] [and] the Microscopy Service at The Jackson Laboratory for expert assistance with the work described in this publication."