Microscopy & Histology

The Microscopy and Histology Core Facilities at La Jolla Institute were developed to help local scientists with their imaging needs in a static or dynamic (in vitro/in vivo) scenario by offering histology and microscopy services and providing support and training to interested researchers. Dedicated personnel can assist in all essential steps of an imaging experiment starting from experimental design, sample preparation through image acquisition and data analysis. The facility offers a range of light microscopes, related imaging systems and image analysis resources for assisted or independent use (upon training). The facility operates on a fee for use basis and is open to all potential users.

Zbigniew Mikulski

Microscopy Core Director

Services

From whole animal imaging to resolving details beyond the diffraction limit, LJI microscopy facility offers one stop shop for all your light microscopy needs. In addition to microscopy services, our staff offers full service histology. Dedicated personnel will take care of your samples to deliver high quality sections which can be digitized and analyzed with the help of our in-house experts. We offer advice on proper sample fixation, processing, embedding of tissues with attention to desired orientation, decalcification of bone tissue, cutting of paraffin blocks, cryosectioning, routine, special and immunostains as well as training in histological techniques.

Instrumentation

Leica SP8 Intravital Multiphoton/Confocal System

This system enables deep tissue imaging of live and fixed specimens with low phototoxicity, using advanced microscopy techniques including confocal and multiphoton imaging. It features a motorized DM6000 CFS microscope, high-speed scanning capabilities, a range of excitation sources, multiple objectives, and comprehensive acquisition software, enhancing research in vivo and in vitro.

Zeiss LSM 880 AIRYSCAN FAST Confocal System

The Zeiss LSM 880, acquired via the NIH Shared Instrumentation Grant (S10OD021831), features enhanced resolution confocal imaging with an Airyscan FAST detector. It supports 3D volume imaging, live cell imaging, and advanced techniques like FRET and FRAP. Various objectives and multiple laser excitation sources enhance its versatility and sensitivity.

Zeiss LSM 780 Confocal System

This inverted confocal microscope offers versatile capabilities, including 3D volume and automated multi-area imaging, as well as live cell time-lapse imaging. It features multiple objectives for various imaging needs, and uses laser excitation from 405 to 633 nm, supported by sensitive detection with bi-alkali PMTs and a spectral GaAsP detector.

Zeiss Axio Scan Z1 Slide Scanner

This automated microscope enables brightfield and fluorescence imaging of whole slides, featuring a barcode scanner for tissue detection and enhanced depth of field. It includes a compact design with a motorized stage, LED illumination, efficient filter sets, and high-resolution cameras, utilizing ZEN2.3 software for image acquisition and analysis.

Imaging Workstations

The facility features three high-end imaging workstations for data analysis, equipped with extensive image and data processing software, including Imaris, Image-Pro, and ImageJ. Each workstation boasts powerful processors, substantial RAM, and dual 32” color-calibrated monitors, all connected to secure LJI servers for data storage and management.

Histology Instrumentation

Trained users have access to a range of histology equipment, including the Sakura automated tissue processor, embedding station, and microtomes. Additional tools include flotation baths, a precision oven, a vibratome, cryostat microtome, antigen retrieval pressure cooker, slide racks, light microscope, automated slide stainer, and automated coverslipper.

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Rates

For all scheduling requests, please contact Zbigniew Mikulski in the form below.

User Support

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Consultation	$106.25	$157.25	$280.50
Training and assistance (added to the base price of the instrument)	$106.25	$157.25	$280.50

Microscopy Support Services

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Imaging workstation (QuPath, Fiji, Imaris, ImagePro, ZEN, Slidebook)	$12.50	$13.00	$18.00
Leica SP8 (confocal/multiphoton imaging)	$50.00	$58.00	$86.00
Leica SP8 after hours 6pm-8am (confocal/multiphoton imaging)	$25.00	$29.00	$43.00
LSM 880 with Airyscan	$39.38	$45.68	$67.73
Zeiss LSM780 confocal	$32.50	$37.70	$55.90
Zeiss LSM780 after hours 6pm-8am	$16.25	$18.85	$27.95
Zeiss AxioZ1 slide scanner	$50.00	$58.00	$86.00
Nanoimager (per hour)	59.38	68.88	$102.13
Keyence	$15.94	$18.49	$27.41
Ami HT	$46.25	$53.65	$79.55
Data Storage (monthly per GB)	$0/no charge	Inquire for Rates	Inquire for Rates
Special Data Services	varies per project	varies per project	varies per project

Histology Core Services

	INSTITUTE AFFILIATE	3RD PARTY NON-PROFIT	3RD PARTY FOR-PROFIT
Histology training	$125.00	$165.00	$295.00
Block with one HE slide (processing, embedding, cutting, and staining with HE)	$12.50	$18.50	$33.00
Block Only (processing, embedding)	$5.63	$8.33	$14.85
Block with one (1) unstained slide	$8.31	$12.30	$21.95
Extra unstained slide	$3.10	$7.00	$11.00
Extra HE slide	$6.88	$10.18	$18.15
Special Stain I (Stains for carbohydrates, connective tissue, muscle fibers, lipids, pigments, minerals, and nerve tissue per slide)	$16.25	$24.05	$42.90
Special Stain II (Stains for microorganism, special cells using silver impregnation)	$17.50	$25.90	$46.20
Frozen Sectioning	$6.19	$9.16	$16.34
Immunostaining (1 target, per slide)	$28.00	$39.00	$70.00
Assay handling, special project (per hour)	$56.25	$83.25	$148.50
Decal	$5.31	$7.86	$14.03

Resources

Contact

For all scheduling requests, please contact Zbigniew Mikulski.