Seattle Children’s Research Institute’s Microscopy and Histopathology Collaborative Laboratory provides access and specialized support for microscopy, image analysis, and histology research needs.
Microscopy Equipment and Services
The CoLab provides access to two laser scanning confocal microscopes, the Zeiss LSM 900 and Zeiss LSM 980. Researchers must first schedule training on the microscope they intend to use before reserving time for access during peak and off-peak hours.
- Peak hours: 9 a.m. to 5 p.m., Monday through Friday
- Off-peak hours: 12 a.m. to 9 a.m. and 5 p.m. to 12 a.m., Monday through Friday; all day Saturday and Sunday
The LSM 900 is equipped with 405, 488, 561 and 640 nm laser excitation lines, three adjustable emission detectors and an upright Axio imager stand. What sets it apart from previous generation confocal microscopes is its inclusion of the Airyscan 2 super resolution imaging capability and deconvolution module. These enhancements allow unprecedented imaging resolution and enhanced speed.
Incorporating the latest AI, the LSM 980 features automated sample placement, focus adjustment and sample area identification. It boasts a wider range of laser excitation lines (405, 445, 488, 514, 561, 594, 639, and 730 nm) for exciting a broad range of fluorophores. It includes a 34-channel spectral detector and NIR detector for sensitivity between 380 to 900 nm and collection of numerous channels simultaneously. It includes an Airyscan 2 detector for super-resolution and fast imaging. The inverted stand is ideal for complex sample types and long-term imaging. The advanced automation and comprehensive imaging modalities make the LSM 980 a versatile asset for a broad range of research endeavors.
The CoLab provides user training on the Zeiss LSM 900 and 980 confocal microscopes. Once trained, researchers may reserve time for self-use on the microscopes during peak and non-peak hours. To request training and other services, visit the CoLab’s iLab page.
The Zeiss Axioscan 7 enables fast and reliable digitization of slides using whole slide scanning capabilities for fluorescence, brightfield and polarization scanning modes. The Axioscan 7’s fully motorized condenser, powerful light sources and sensitive cameras allow for 24/7 automated and contactless scan performance, whether users have many similar slides or mixed applications to process. The system accommodates microscope slides with 1″x3″, 2″x3″, 4″x3″ dimensions as well as thickness ranging from 0.8 to 1.3 mm. Axioscan 7 software is designed to process large amounts of raw data in the range of several terabytes, and guides users through profile development for automated tissue detection and focused imaging.
Histology Equipment and Services
Histopathology services provided by the CoLab include tissue processing, embedding, sectioning, basic staining, immunohistochemistry as well as multiplex immunofluorescence. Consultation on experimental setup, slide preparation and data analysis are also available.
The CoLab provides consultations and technical support on histopathology services and experimental design.
The CoLab provides paraffin tissue processing with or without decalcification.
Please consult CoLab staff if you need decalcification.
The CoLab provides both cryosectioning and paraffin sectioning.
The CoLab has a vibratome available for tissue sections. Please contact the core to schedule usage.
The CoLab provides Hematoxylin and Eosin (H&E) staining. Please consult with CoLab staff for other special staining.
The CoLab uses a Roche Ventana Discovery autostainer as well as a Leica Bond Rx autostainer for immunohistochemistry and immunofluorescent tissue staining protocols. The Leica Bond Rx can also be utilized for semi-automating GeoMx and CosMx slide prep workflows.
For all immunohistochemistry requests, please consult the histology team to discuss antibody optimization and project budgeting
The CoLab provides automated in-situ hybridization using a Leica Bond.
Request Training and Services
Microscopy and Histopathology training, services and self-use are available to internal and external users. To request training for the confocal microscopes, slide scanning services, or histology services, please visit the CoLab’s iLab page.
For information on how to access iLab, refer to this guide.
Acknowledging Core Contributions
When citing the Microscopy and Histopathology CoLab, we recommend the following language: Seattle Children's Research Institute Microscopy and Histopathology Collaborative Laboratory, RRID:SCR_025489.
If you need more information for your grant, please contact the Microscopy and Histopathology CoLab staff.
General Expectations for Submitting Samples for Histology Services
Please see the CoLab's sample submission page for guidance on how to prepare and submit FFPE, OCT and IHC samples to optimize results.
Access and Contact Information
Address for confocal microscopes and slide drop-off* for Axioscan
Jack MacDonald Building (JMB)
1900 Ninth Ave.
Seattle, WA 98101
* Slide drop-off is in JMB 745, and drop-off dates must be approved ahead of time by CoLab staff.
Address for histology services
B. Wayne Hughes Building
1920 Terry Ave.
Seattle, WA 98101
- Microscopy and slide scanning support: Aarya.VaikakkaraChithran@seattlechildrens.org
- Histology: SRRhistology@seattlechildrens.org
Staff Support
The Microscopy CoLab provides consultation on services, experimental design and analysis, as well as technical support for microscopy services. These services may be requested in iLab.