CDR Facilities

The CDR is comprised of 26,000 square feet of space designed and equipped specifically for studies of biochemistry, molecular biology and morphology of the Central Nervous System. The area consists of eight laboratories, electron microscope (EM) and confocal microscopy facility, darkrooms, three walk-in cold rooms, four tissue culture facilities, a glassware washing unit, segregated area for radioisotope studies and tissue processing and histology facility. 

Cytometry and Cell Sorting Facility

Flow-cytometry has the unique ability to identify specific subtypes of extracellular vesicles (EVs), while also identifying the cell of origin of a given vesicle. Multiple simultaneous parameters can be obtained via the Cytometry and Cell Sorting Facility at the CDR. The facility houses the Invitrogen Bigfoot Spectral Cell Sorter Fluorescence Activated Cell Sorter (FACS), an advanced state-of-the-art instrument. FACS is utilized to acquire optical measurements using different lasers to detect flurophores with a high level of precision, giving our researchers access to powerful and adaptable flow cytometry and cell sorting technologies. FACS is also used to analyze brain derived EVs in blood, with the aim to identify novel biomarkers at early stages of neurodevelopmental, neurodegenerative, and psychiatric disorders. The Bigfoot allows spectral sorting and spectral analysis not only at the level of the cell to identify and isolate specific cell types, but also at the level of vesicles, both intracellular and extracellular. Central to our research, is the ability to analyze the various defined populations of intracellular and extracellular compartments from cells in culture, brain tissue, and blood. The instrument allows our researchers to obtain the highest-quality data from every sample to achieve increasingly challenging scientific goals defined within ongoing projects in the CDR and extend those research directions.

The Invitrogen Bigfoot Cell Sorter with Sasquatch Software (SQS) has 9 lasers and 60 detectors for analysis of cell populations labeled with fluorescent proteins.
The Invitrogen Bigfoot has sort rates of 70,000 events per second. It can sort a 96-well plate in less than 8 seconds and a 384-well plate in less than 11 seconds. It offers rapid cell sorting in culture, brain tissue and blood.

Confocal Microscopy Facility

The Center for Dementia research is equipped with two laser scanning confocal microscopes, an LSM 510 Meta System and an LSM 880 System, both from Zeiss Microscopy. These systems are used primarily for imaging fixed brain tissue and cell cultures stained with multiple fluorophores. Both systems have heated chambers and CO2 inputs to allow for live imaging of cells in culture with dynamic dyes and can create videos to show changes in real time. The microscopes have 3 lasers for green red and far-red excitations. The LSM880 can also image blue dyes using a LED and is equipped with the additional capability to make tiled images in a single plane or in z-stacks so that the whole tissue section or cell culture can be reproduced as a 3D rendering. Images can also be analyzed for colocalization between fluorophores or detect relative intensities and sizes of cells and vesicles being studied. CDR confocal microscope analysis has been applied to human brain and mice modeling Alzheimer disease and related disorders (Huntington’s, Parkinson’s, ALS etc. Cell lines of both human and mouse origins, including fibroblasts from human patients of Familial Alzheimer’s and Down’s syndrome, and primary neurons and blastocysts from mice, are also analyzed in both live imaging and fixed contexts.

The Zeiss LSM510 has multiple objectives for both low and high power air and oil objectives from 10X to 100X, used for imaging 3 different fluorophores. System can z-stack images with projections in 3D.
The Zeiss LSM880 has multiple objectives from 10X to 100X for low and high power and frame resolution upto 8192X8192, imaging 4 different flurorophores.

Electron Microscopy (EM) Facility

The Electron Microscopy (EM) Facility at the CDR, headed by Dr.Chris Goulbourne is a core facility that provides EM service to investigators. The facility houses a ThermoFisher Talos L120C TEM with 2D imaging capability, dual axis electron tomography for 3D ultrastructural evaluation and cryo EM. Services offered include ultrastructural evaluation in 2D and 3D, protein localization using immunogold techniques and cryogenic evaluation of proteins, viruses, and cellular architecture. Additionally, the facility offers guidance and sample preparation for employing correlative light and electron microcopy (CLEM) and nano secondary ion mass spectrometry (NanoSIMS) for tracking stable isotope tagged molecules. Sample preparation instrumentation includes a Leica UCT ultramicrotome and ThermoFisher Mark IV Vitrobot, as well as a dedicated high-performance workstation for processing 3D data sets using Amira and Imod software. The services of the facility are currently available to external academic institutes and industrial facilities on a fee-for-use-basis. Additional information can be obtained by contacting Dr. Chris Goulbourne at

The Talos L120C TEM is operated from a control room where the microscope workstation is used for taking images using TEM Imaging and Analysis (TIA) software that are stored on the support PC. The control panels are used for positioning the stage, performing alignments, altering intensity, focusing the image and controlling the Ceta 16M Camera to take images.
The FEI Talos L120C TEM has magnification between 25X upto 650,000x and 0.2nm line resolution. Capabilties include electron tomography for 3D ultrastructural evaluation, regular 2D imaging and cryoelectron microscopy.

TEM Images

Cryo electron microscopy of extracellular
vesicles isolated from a 12-month-old mouse brain. Magnification 45000x.
Levy Laboratory
Neuron and glia nuclei that have been immunogold labeled using an anti histone antibody that has been silver enhanced. Magnification 4300X. Nixon Laboratory Serial Block Face Scanning Electron Microscopy 3D reconstruction of 50µm thick mouse cortex using a ThermoFisher Apreo Volumescope. Nixon Laboratory

Genomics Facility

The Genomics Facility at the CDR, headed by Dr. Stephen Ginsberg enables researchers to conduct a wide variety of genomics paradigms. These include laser capture microdissection (LCM) for downstream applications including quantitative PCR (qPCR) performed at the CDR, as well as RNA sequencing (RNA-seq) and Nanostring nCounter performed by our partners at the New York University Grossman School of Medicine Genome Technology Center. LCM instrumentation in the CDR enables microisolation of desired cell types, including neurons visualized via brightfield or fluorescent optics either through histochemical (e.g., Nissl or hematoxylin and eosin) or immunocytochemical labeling.

Histology Facility

The Histology Facility at the CDR, headed by Arthur Saltzman provides researchers with a range of services for histology. These include tissue preparation, embedding, sectioning, histochemical staining, and immunohistochemistry. We offer paraffin, frozen (fixed or fresh), and vibratome sectioning. Tissue sections can also be prepared and processed for downstream DNA, RNA, and/or protein extraction. Sections can be mounted on standard or charged slides for histopathology or molecular and cellular procedures. Frozen sections can be adhered to PEN-membrane slides for laser capture microdissection. Staining options include hematoxylin and eosin, special stains, and immunocytochemical preparations.

Leica CM1860 UV is a cryostat which produces tissue sections of a thickness between
1-100um. It has a temperature range of 0 °C to -35 °C. The cryostat is protected by ozone-free UVC disinfection and an antimicrobial coating that reduces exposure to surface pathogens.
Thermo Shandon Finesse rotary ME microtome has a section thickness range between 0.5-100 um. Sections can also be made using pre-programmed settings. The microtome allows for standard wax as well as resin and plastic sectioning. Leica ASP300 Tissue Processor is a fully enclosed tissue processor capable of processing up to 300 cassette-embedded samples at a time with a paraffin melt time of 10 hours. This processor features 3 paraffin baths and 15 programs for up to 10 reagents.