ALMC Slide Scanning Service

The ALM Core provides staff assisted slide-scanning services using a ZEISS Axioscan7 slide scanner, located in KCRB. The scanner is equipped with a color camera for brightfield imaging and a Hamamatsu Orca Flash 4.0 monochrome sCMOS cameras for fluorescence imaging. Click here for more detailed description of the system. 

We can scan with a range of objectives and detect fluorescence across the visual spectrum and NearIR. The system is ideal for thin FFPE or cryostat sections. See our instrumentation page for a list of our other systems. 

Members of the 博彩网站 research community can submit requests for slide scanning via our Request Services tab in iLab. Choose the form called "Staff-assisted Slide Scanning". 

Members of the Knight Cancer Institute can contact us at almc@ohsu.edu about prioritized access. 

External users should reach out to almc@ohsu.edu to inquire about access to our services.

We transfer your data to OneDrive or DropBox, but due to the large size of the slide scanning files, we strongly suggest that labs with regular slide scanning needs establish a networked storage server at the Advanced Computing Center.

General considerations for sample preparation

Do’s

  • Use standard 1x3 or 2x3 inch glass slides. Please note we reject broken slides for safety reasons. 
  • Clean your slides and coverslips. The autofocusing routine is easily fooled by dirt. Autofocusing failures result in blurred images and require rescans that incur further charges. We charge our regular staff rate for cleaning slides and we will take our time…

Don’ts

  • No PHI on slide labels and sample carriers!
  • Do not wrap slides with tape or labels.
  • Coverslips cannot overhang the slides.

Special considerations for fluorescent sample preparation

Do’s 

  • Include at least one ubiquitous stain. The automated focusing routine requires signal across all of the tissue. We recommend a blue DNA staining step for this purpose. Refrain from using mounting media containing DNA dye as it gives very variable results from slide to slide and across each slide.
  • For 5-channel multiplexing use Blue, Green, Orange-Red, Far-Red, and NearIR fluorophores.
  • Use your brightest marker for the NearIR channel as it has the lowest sensitivity. 
  • Use single stain combination per slide. Each run can only scan with one set of imaging parameters.
  • Carefully clean your coverslips before mounting. Dirt under the coverslips easily throws off autofocusing.
  • Clearly indicate wet mounting. We expect coverslips to be firmly attached. If not alerted, we may destroy your sample when trying to clean your slides!

Don’ts 

  • Do not combine Dark-Red fluorophores with Orange-Red and Far-Red fluorophores due to channel crosstalk. Dark-Red fluorophores are Alexa594, TexasRed, or similar, and Orange-Red fluorophores are Alexa555, Alexa 568, Cy3, or similar. Choose either for combination with Green fluorophores, but only use Orange-Red fluorophores with Far-Red fluorophores, like Alexa647, Cy5, or similar