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 three confocal microscopes, two automated high-throughput imaging systems, a cleared tissue light-sheet microscope and two dedicated image analysis workstations. Researchers must first schedule training on the microscope they intend to use before reserving time for access. The microscopes are available at peak and off-peak hours that include:
- 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
- Yokogawa CSU-W1 SoRa (Spinning Disk; inverted): A super-resolution system built on a motorized Nikon Ti2-E inverted microscope. Optimized for high-speed, live-cell imaging using SoRa optical pixel-reassignment. Features a 7-line high-power laser launch (405/446/488/518/577/639/748), ultra-sensitive Hamamatsu ORCA-Quest 2 qCMOS camera, and a stage-top incubation system (CO2/Temperature/Humidity).
- Zeiss LSM 980 (Inverted): Optimized for automated, high-resolution imaging. Features an inverted stand with AI-powered sample finding (automated placement, focus, and identification). Equipped with 8 laser lines (405nm to 730nm), NIR detectors (up to 900nm), Airyscan 2 super-resolution, and a deconvolution module.
- Zeiss LSM 900 (Upright): Situated on an Axio Imager stand, this system is ideal for routine high-resolution confocal work. Includes 4 laser lines (405, 488, 561, 640 nm) and Airyscan 2 super-resolution capability.
- LifeCanvas SmartSPIM Light-Sheet: Specialized for high-resolution volumetric 3D imaging of whole organs and large tissues. Utilizes patented axial sweeping for homogenous PSFs across the field of view. Supported by NIH S10 grant 1S10OD038341-01.
- Please remember to acknowledge use of the core's light sheet microscope in talks, posters, and publications which include data generated in the Microscopy and Histopathology CoLab.
- Suggested text: "Light sheet microscopy was performed in the SCRI Microscopy and Histopathology CoLab (RRID:SCR_025489). This work utilized a LifeCanvas Technologies SmartSPIM Light-Sheet Microscope purchased with funding from NIH S10 grant 1S10OD038341-01."
- SmartBatch+: A high-throughput system combining electrophoretic tissue clearing and immunolabeling. Processes up to 12 mouse brains or 4 rat brains simultaneously using eFLASH technology.
- SmartClear II Pro: Dedicated electrophoretic tissue clearing device for rapid batch processing of various tissue types.
- Note: Tissue clearing reagents are available directly through the CoLab.
- ImageXpress Nano: An automated system for multi-well plate screening. Features LED channels (DAPI, FITC, Cy3, Texas Red, Cy5) and MetaXpress 6 modules for automated analysis of nuclei count, neurite outgrowth, cell scoring, translocation, and live/dead assays.
- Zeiss Axioscan 7: High-throughput slide digitization. Capacity for 100 slides per scan with objectives from 5x to 40x. Supports brightfield, polarized, and 7-channel fluorescent imaging (385nm to 735nm).
Microscopy services also include training and support with image visualization and analysis. The CoLab provides the following image analysis capabilities, available for scheduling in iLab:
- Imaris 11 core facilities package with a floating license manager
- Zeiss Zen 3.12 including LSM Plus and Airyscan Joint Deconvolution modules
- NIS Elements 6.10 including GA3, HCA, Jobs
- Zeiss Arivis pro 4.1.0 (formerly Vision4D)
- 3D Slicer including SlicerMorph extension
- Fiji/ ImageJ
- QuPath
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), 7th Floor
1900 Ninth Ave.
Seattle, WA 98101
* Slide scanning drop-off is at JMB 7th Floor, Bench 36, and drop-off dates must be approved ahead of time by CoLab staff.
Address for histology services
Jack MacDonald Building (JMB), 7th Floor
1900 Ninth Ave.
Seattle, WA 98101
- Microscopy and slide scanning support: [email protected]
- Histology: [email protected]
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.