Leica Bond RXM auto stainer is a fully automated system designed for immunohistochemistry (IHC) and in situ hybridization (ISH) testing. It is used to examine tissue slices for specific antigens or nucleic acid sequences to diagnose disorders, especially malignancies. The system automates the entire staining process, including tissue preparation, chemical application, and detection, without requiring user intervention. This automation enhances uniformity, reduces human error, and saves time for lab staff and pathologists. The Bond RXM is particularly useful for research applications, allowing for the design of custom protocols and the use of a variety of reagents. It is compatible with multiple detection systems and supports multiplexing, enabling the visualization of multiple markers on a single slide. The Bond RXM is an open system, providing flexibility in protocol and reagent selection, making it suitable for a wide range of research needs.

Citation language used for Leica Bond RXm Autostainer - Acknowledge the Northern New England Clinical & Translational Research Network (NNE-CTR) supported the purchase of the autostainer. National Institute of General Medical Sciences Clinical and Translational Research IDeA (CTR) Award (grant number U54GM115516) was used to purchase the autostainer.

Confocal Microscopes are an advanced optical imaging device that enhances the resolution and contrast of micrographs by eliminating out-of-focus light. It uses a spatial pinhole to focus on a single plane of the specimen, allowing for the capture of multiple two-dimensional images at different depths, which can be reconstructed into three-dimensional structures. This technique is particularly useful in biological and materials sciences for detailed imaging of samples.

• Nikon A1R-ER Confocal Microscope - The Nikon A1R-ER is a point-scanning confocal that contains a dual scanning system built into the scan head.  It has both a high-resolution galvanometer scanner and a high-speed resonance scanner.  The galvanometer scanner scans a single illumination point over the image field as fast as 8 frames/sec for a 512 x 512 pixel field and can be used to acquire high spatial resolution images at up to 4096 x 4096 pixels.  The resonance scanner can be used to acquire highly temporarily resolved images at up to 15 frames/sec at 1024 x 1024 pixels resolution or 420 frames/sec in band scan acquisition mode at 512 x 32 pixels resolution.  A deconvolution module provides for Enhanced Resolution of acquired images.  Signal is detected with 2 GaAsP and 2 high sensitivity PMTs for visible lasers, emission sets for 450/50, 525/50, 600/50 (UV/GFP/RFP/Cy5) and the system is set on an inverted Ti2 stage with Perfect Focus System (PFS4) allowing for live cell work. The Ti2 is an exceptionally stable, drift-free platform with hardware-triggering capabilities and high-speed imaging applications allowing quick complete slide scanning.  This confocal is driven by the NIS-Elements software platform and equipped with JOBS, a macro building software which allows for custom high through-put imaging. Other System Components: LUNV laser launch with 405nm, 445nm, 488nm, 514nm, 561nm, 633nm solid state diode lasers (all 20mW output at the fiber tip), Hybrid resonant and Galvano scanhead for simultaneous FRAP, photostimulation and optogenetics, Ti2 Inverted Microscope with 25mm FOV and the Perfect Focus System 4, Live-cell chamber – stage-top incubator for CO₂, temperature and humidity control, 4x, 10x, 20x, 40x air, LWD 40x oil, 40x water, 60x oil Objectives, Spectral Detector and spectral unmixing for detection of signal separated by less than 5 nm, Epifluorescence components and Fluorescence SpectraViewer.

Citation language used for Nikon A1R-HD Point Scanning Confocal - Confocal microscopy was performed on a Nikon A1R-HD point scanning confocal supported by NIH award number 1S10OD025030-01 from the Office of Research Infrastructure Programs.

• Nikon C2 Confocal Microscope - (located in Given Bldg, Rm E015D) The Nikon C2 Confocal Microscopy System was purchased with funds from the COBRE “Center for Neuroscience Excellence” grant (P30 RR032135 / P30 GM 103498, Imaging Core 026354) in 2015. The C2 system is based on a Nikon Ti-E inverted platform equipped with Plan Apo and Plan objective lenses with DIC capability, including a 10X/ 0.45 NA, 20X/ 0.75NA, 40X/ 1.0 NA and 60x/ 1.4 NA. Solid-state, fiber coupled lasers provide excitation at 405nm, 488nm, 561nm and 640nm. Three photomultiplier tubes can capture fluorescent images simultaneously, along with one dedicated transmitted detector. Emission filters are set at 445/35nm, 525/50nm, 600/50nm and >660nm. The 405nm and 640nm channels must be collected separately. Nikon Elements software provides the user interface. The Nikon C2 is located in the basement of the Given Building, E015D. Please contact Todd Clason 656-0413 for training and further information.
• Zeiss LSM7 Multiphoton Microscope - (located in Given Bldg, Rm E015C) The Zeiss LSM-7 MP Dedicated Multiphoton has four non-descanned PMT detectors, two of which make up the highly sensitive gallium arsenide phosphide Zeiss  BiG detector. Multiphoton excitation is generated by a Coherent Chameleon Vision II Titanium Sapphire pulsed IR laser, with dispersion compensation, and tunable from 720-950 nm. The stage is a motorized Prior Z-deck, which is fully integrated into the Zeiss Zen software. A 20X Plan Apo 1.0 NA DIC VIS-IR water immersion lens is the main objective lens. The system frame is a Zeiss Axio Examiner, specifically optimized for multiphoton microscopy. The system is located in the basement of the Given Building, E015C. This system was purchased in 2012 with funds from an NIH shared instrumentation grant (S10 ODO10583). Please contact Todd Clason 656-0413 for training and further information. Citation language for Zeiss LSM7 Multiphoton Microscope - This system was purchased in 2012 with funds from an NIH shared instrumentation grant (S10 ODO10583).
• Yokogawa Spinning Disk Microscope - (located in Given Bldg, Rm E015B) The Yokogawa CSU-W1 spinning disk confocal system is coupled to a Nikon Eclipse NI-E upright microscope with two Andor EM CCD detectors for simultaneous two-channel imaging. It was purchased with funds from an NIH shared instrumentation grant in 2014 (S10 ODO17969). Three laser lines are available, 488 nm 561 nm and 640 nm. The Yokogawa CSU-W1 has two water-immersion objectives: a Nikon Apo LWD 25X/1.1NA, and a Nikon Fluor 60X/1NA, both with 2mm working distance. This instrument is designed for fast image collection in live tissue samples, with rates in excess of 50 frames/sec at 512 x 512 pixels resolution. With its large-diameter Nipkow disk, the CSU-W1 provides a significant field of view with outstanding image quality. NIS-Elements is the software platform, and a full perfusion system is available. Please contact Todd Clason 656-0413 for training and further information.

ECIS is a real-time, label-free, impedance-based method to study cell behaviors in tissue culture. These include monolayer barrier function, cell growth rates and viability, wound-healing migration and other behaviors directed by the cell’s cytoskeleton. The ECIS approach has been applied to numerous investigations including measurements of endothelial monolayer permeability, in vitro toxicity testing as an alternative to animal testing, the invasive nature of cancer cells, and signal transduction involving GPCR’s for modern drug discovery.

Our ECIS system (from Applied BioPhysics, Inc. Troy, NY) measures impedance, resistance, and capacitance in cultured cells grown on specially-fabricated chamber slides fitted with gold film-coated microelectrode. The cell electrical parameters are measured at various frequencies from 64-64,000 Hz, and indicate barrier function (adherence of cells to each other through junctional complexes), and adherence of cells to the substrate (capacitance). This system provides a continuous temporal assay of the physiologic state of cultured cells. The effect of the addition of chemical compounds, pharmaceuticals, or other reagents on cell physiology and morphology can then be monitored. The ECIS system in the MIC is housed adjacent to an Olympus IX70 inverted microscope, for convenient visual assessment of the cells.

SEM is a type of electron microscope that uses a focused beam of electrons to produce high-resolution images of a sample's surface. It scans the surface with the electron beam, which interacts with atoms in the sample to produce various signals that reveal information about the surface topography and composition. SEM is widely used in various scientific fields for analyzing materials and nanomaterials, providing detailed insights into their structure and properties.

• Scanning Electron Microscope - SEM - The JEOL 6060 scanning electron microscope is used for investigations of bulk specimens. 

TEM is a powerful microscopy technique that uses a beam of electrons to create detailed images of specimens. This method allows for the visualization of structures at a significantly higher resolution than that achievable with light microscopes, enabling the examination of materials at the atomic level. TEM is widely used in various scientific fields, including materials science, biology, and nanotechnology, to study the internal structures and composition of materials. 

• Transmission Electron Microscope - TEM - The JEOL 1400 Transmission Electron Microscope is a high-contrast, high-resolution instrument utilizing a LaB6 filament, and capable of operating at accelerating voltages up to 120 kV.

• HALO Workstation - This is a computer workstation equipped with Indica Labs HALO image analysis package and NIS Elements software.  HALO is currently equipped with the following image analysis modules: Area Quantification FL, Area Quantification, Deconvolution, FISH Break-Apart/Fusion, FISH-IF, FISH, HighPlex FL, ISH IHC

Citation language used for Indica Labs HALO Image Analysis Software - Acknowledge the Northern New England Clinical & Translational Research Network (NNE-CTR) supported the purchase of HALO. National Institute of General Medical Sciences Clinical and Translational Research IDeA (CTR) Award (grant number U54GM115516).

• MetaMorph / Volocity / N-STORM /Stereo Investigator image analysis Workstation - This workstation contains four high end image analysis software packages: Universal Imaging MetaMorph image analysis software (MetaMorph). Improvision Volocity software, for 3D analysis and reconstruction. Stereo Investigator software from MicroBrightfield, Inc. for computer-assisted stereological analysis. N-STORM analysis software within NIS elements platform and Object Classifier.

Citation language for Stereo Investigator - Acknowledge MBF Bioscience and Jack Glaser who were benefactors of the generous gift of Stereo Investigator. 

• FlowJo Workstation - Workstation containing FlowJo 10 and FlowJo 11 software for flow cytometry data analysis. Located in the CBSR common space at touchdown desk and via remote access. Contact MIC for instructions and passwords.

LCM is a technique used to isolate specific cells from tissue samples under microscopic visualization. It allows researchers to collect pure cell populations without contamination, preserving tissue morphology for high-quality analysis.

• Arcturus XT-Ti Laser Capture Microdissector - The Arcturus XT-Ti Laser capture microdissector is used for specifically removing desired cells from a tissue section for subsequent molecular analysis. Both gentle infrared cell capture and rapid ultraviolet laser cutting are included on this one instrument. Cells are captured automatically using an interactive pen-display monitor and trackball-actuated stage. The microdissector is integrated onto a Nikon Eclipse-Ti inverted microscope, equipped with 2X, 10X, and 40X objective lenses. Fluorescence illumination is accomplished with a Lumen Dynamics X-Cite lamp module with liquid guide. Fluorescence cubes for uv excitation (325-375nm Ex/420 Em), blue excitation (450-490nm Ex/515nm Em), green excitation (510-560 nm Ex/590nm Em), and red excitation (590-650nm Ex/663-738nm Em) provide the ability to microdissect and capture fluorescently labeled cells within tissues. A second ccd camera has been added to a side port on the microscope for high resolution acquisition of brightfield and fluorescence images. Tissue sections can be microdissected from plain glass slides, PEN membrane coated slides, and Framed, coated slides.

• Deltavision Restoration Microscope - (located in Given Bldg, Rm E015E) - The DeltaVision Restoration Microscopy System consists of an inverted Olympus IX70 microscope combined with a set of motorized filter sets and a precision stage. The system has carefully integrated deconvolution software, which allows for greatly enhanced wide-field fluorescent images. This system is designed to provide time-lapse capabilities in live cells or tissues (<100 micron thick) with minimal photo-bleaching. Filter sets for blue, green, red and far red probes are available, along with 20X 0.5NA air, 20X 0.8NA oil, 40X 1.35NA oil, 60X 1.2 A water, 60X 1.4NA oil and 100X 1.4NA oil lenses. Image capture is accomplished with a Photometrics Coolsnap HQ camera.  Please contact Todd Clason 656-0413 for training and further information.
• Leica VERSA8 Whole Slide Imager - This highly versatile instrument is an automated scanning microscope and image generation scanning system. Some of its features include: integrated brightfield and fluorescence scanner; two high quality CMOS cameras for brightfield or fluorescence image acquisition; batch set-up and automation for unsupervised scanning of up to 8 slides; fluorescent scanning of up to 7 fluorophores/slide; and a wide range of Leica quality objective lenses (1.25, 5, 10, 20, 40, and 63X). Software allows low magnification overview of an entire sample, with high resolution “zoom in” feature to analyze cellular features.

Citation language for Leica-Aperio VERSA whole slide imager - Acknowledge the College of Medicine Shared Instrumentation Award (DT) that was used to purchase the Leica-Aperio VERSA whole slide imaging system.

• Leica MZ16F Stereo Microscope
• Olympus BX50 Upright Microscope - Olympus BX50 microscope with Teledyne QImaging MicroPublisher6 digital camera. Features include: Epi-fluorescence objectives (10X, 20X, 40X, 60X, 100X), Phase Contrast, Double and triple fluorescence staining possible, Computer and software for image management and archiving. This microscope contains bandpass filters for ultraviolet, blue and green fluorescence emissions. These filters allow single, or simultaneous double and triple fluorescence imaging. A Teledyne QImaging MicroPublisher6 cooled digital camera with interface to a PC allows for capture of digital images.
• Olympus IX70 Inverted Light Microscope - The microscope is fully equipped for epi-fluorescence and phase contrast microscopy with long working distance objective lenses and condenser lens. A Zeiss AxioCam 202 Mono 2 megapixel CMOS camera and computer system was recently added for digital image acquisition. The system is also supported by an Applied Biophysics ECIS ZTheta module for tracking and measuring cell impedance.
• Olympus SZX12 Dissecting Microscope

• Cryostat - We use the Thermo Shandon Cryotome E for sectioning fixed tissue or unfixed nonhuman tissue.
• JB4 Microtome - We use the Leica Hard Plastic Microtome (Leica RM 2165) which is a fully motorized rotary microtome for routine paraffin and hard plastic sectioning.
• Leica Paraffin - We use the Leica RM2145 which is a semi-electric paraffin microtome as well as the Leica 2030 which is a fully manual paraffin microtome.
• Ultramicrotomes - We use Reichert Ultracut Ultramicrotomes 1, and 2.

NanoString's GeoMx Digital Spatial Profiler (DSP) is a cutting-edge technology that enables the analysis of RNA and protein in tissue samples. It combines traditional immunofluorescence techniques with digital optical barcoding technology to perform highly multiplexed, spatially resolved profiling experiments. The GeoMx DSP captures tissue morphology and selects regions of interest (ROIs) for high-plex profiling, allowing researchers to obtain insights about the spatial distribution of gene expression patterns, cellular diversity, and interactions within tissues. This technology is particularly useful for studying intricate biological mechanisms, including growth, disease advancement, and reaction to therapy. GeoMx is a versatile technology that finds utility across diverse domains such as cancer research, neuroscience, immunology, and developmental biology. It empowers researchers with a potent means to explore the spatial arrangement of gene expression in tissues, thereby enhancing our comprehension of intricate biological systems.

Citation language for the Nanostring GeoMX Digital Spatial Profiler - Please acknowledge the Northern New England Clinical & Translational Research Network (NNE-CTR) supported the purchase of the GeoMx. National Institute of General Medical Sciences Clinical and Translational Research IDeA (CTR) Award (grant number U54GM115516).

The Akoya PhenoCycler system is a high-speed imaging and automated cycling solution that enables spatial analysis for discovery biology. It allows for the detection of over 40 biomarkers in a single tissue section at single-cell resolution. This system is part of an integrated spatial biology workflow that includes single-step tissue staining, image acquisition, and on-board processing. The PhenoCycler-Fusion 2.0 technology uses antibodies conjugated to a proprietary library of oligonucleotides called Barcodes, enabling customizable panels of up to 40+ PhenoCycler-Fusion Assays to be combined for a single tissue staining reaction. This technology is particularly useful for studying tumor heterogeneity and microenvironment, as well as for spatial phenotyping across whole slides to detect protein in situ. 

Citation language Akoya Phenocycler Fusion - Acknowledge the Northern New England Clinical & Translational Research Network (NNE-CTR) supported the purchase of the Phenocycler Fusion. National Institute of General Medical Sciences Clinical and Translational Research IDeA (CTR) Award (grant number U54GM115516).

Atomic force microscopy (AFM) is a very-high-resolution type of scanning probe microscopy with demonstrated resolution on the order of fractions of a nanometer, more than 1000 times better than the optical diffraction limit.

• Asylum Atomic Force Microscope - The Asylum Research MFP-3D BIO AFM allows investigation of biological/materials surfaces at high resolution.
• Cypher Atomic Force Microscope - The Asylum Research Cypher ES boasts exceptional performance and full environmental control features. It masters high resolution imaging with speed and stability while containing an easily operatable environmental chamber to control gas or liquid environments, at temperatures from 0-250°C, and in some of the harshest chemical environments. The Cypher ES is the ultimate AFM for the most demanding experimental requirements.

Citation language AFM- Atomic force microscopy was performed on an Asylum Research MFP-3 D BIO supported by NIH award number S10RR025498 from the Office of Research Infrastructure Programs.

Nikon n-Storm Super Resolution Microscope consists of a Nikon Ti-E TIRF inverted microscope base with laser modules delivering excitation at 405 nm, 488 nm, 561 nm, and 647 nm, and a high sensitivity Andor iXON3 DU897 EMCCD camera. This instrument provides resolution in the fluorescence mode of 20 nm lateral and 50 nm axial. Both fixed and live cell preparations can be imaged, as well as imaging in three dimensions. 

description needed here...analyzer

Citation language for Cytek Aurora - Flow cytometry was performed on a Cytek Aurora Flow Cytometer supported by NIH award number S10-ODO026843.

description needed here...analyzer

The MACSQuant VYB is a compact benchtop flow cytometer. It has 3 spatially-separated laser beams: 405 nm (violet) diode laser, 488 nm (blue) diode pumped solid state (DPSS) laser, and 561 nm (yellow) diode laser, with detection of 10 optical parameter. This instrument performs absolute counting, multiparameter cell analysis and rare cell analysis (using an integrated Cell Enrichment Unit), and it is fully automated. It is the choice instrument for performing multiparameteric analysis of fluorescent protein expressing cells. This instrument uses MACSQuant v5 Software.

The ZetaView is a nanoparticle tracking analyzer. More description needed here...analyzer

Citation language for ZetaView TWIN NTA - Nanoparticle tracking analysis was performed on a Particle Metrix ZetaView TWIN NTA supported by NIH award number S10-ODO02976.

equipment description to come...