Digital Pathology Services

Slide Imaging and Digital Image Analysis

We offer brightfield and fluorescent slide imaging, digital image analysis, and training in the independent use of our fluorescent slide scanner and image analysis software.

We provide images to the user in HALO Link, a web-based image management software that offers easy sharing and collaboration and seamless integration with Indica Labs’ HALO image analysis software.
 

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Services  |  Instruments

Schedule With Us

To schedule digital pathology services, or to get more information about how we can work with you, view our rates and scheduling page or contact our digital pathology team:

Services

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HALO image analysis

Investigators can use HALO image analysis software with chromogenic and fluorescent images from a variety of imaging platforms. With this software, users can fuse single-channel images and tiles and register or overlay parallel images for simultaneous analysis. Users can also annotate images to denote separate layers for analysis or classifiers used to create annotated areas for analysis based on distinctive colors or textures. HALO offers gross area quantification or nuclear detection for cell quantification. Investigators can view the results of analysis as summary data or as cell-by-cell object data, export it to Excel for further analysis, or conduct further spatial/proximity analysis within HALO. 

The following image analysis modules are available for use on the HALO workstations: 

  • Area quantification (chromogenic and fluorescent) 
  • Cytonuclear (chromogenic and fluorescent) 
  • Deconvolution 
  • FISH and ISH 
  • FISH-IF and ISH-IHC 
  • Multiplex IHC and Highplex FL 
  • Immune cell 
  • Membrane (chromogenic and fluorescent) 

Remote use of the Halo analysis workstations, while using a VPN connection, is also supported. 

We offer training for the independent use of our Aperio FL fluorescent slide scanner and HALO image analysis software, in addition to providing these services for a fee.

At the HALO online training portal, find tutorial videos, user guides, technical documentation, webinars and other learning resources for learning our HALO software.

Microscopic image of cells
Analysis overlay on tissue stained with the 5TC_1 panel Image by Paul Kong / Experimental Histopathology shared resource
Brightfield and fluorescent slide imaging

Brightfield imaging is a standard scanning technique that visualizes the specimen against a uniformly-lit background via an external light source. We can image standard 75mm x 25mm microscope slides at magnifications of 20x up to 63x (dry). Instruments that are capable of brightfield imaging are our Aperio AT and Aperio VERSA 200.

Fluorescent imaging uses filter cubes, which allow specific wavelengths of light from the source to excite fluorophores of interest in the sample. Our Aperio FL and Aperio VERSA 200 are capable of imaging up to three fluorophores, plus a nuclear counterstain (DAPI).

Microscopic image of cells
Sample under brightfield and fluorescent imaging Image by Paul Kong / Experimental Histopathology shared resource
Training

We offer training for the independent use of our Aperio FL fluorescent slide scanner and HALO image analysis software, in addition to providing these services for a fee.

At the HALO online training portal, find tutorial videos, user guides, technical documentation, webinars and other learning resources for learning our HALO software.

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Instruments

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Aperio AT Turbo

Our Aperio AT Turbo scanner offers high-throughput 20x and 40x brightfield slide scanning with 200-slide capacity.

Aperio FL

Our Aperio FL slide scanner offers 20x and 40x fluorescent slide scanning with five-slide capacity. It provides images as merged .svs files. The Aperio FL contains filters for DAPI, FITC, CY3, Texas Red and CY5, which offers imaging of a wide range of fluorophores. This instrument can perform whole-slide fluorescent scanning of up to four fluorophores, including DAPI. We offer training to users for independent use of this instrument.

Aperio VERSA 200

Our Aperio VERSA 200 digital pathology scanner offers high-throughput 20x, 40x and 63x (dry) brightfield and fluorescent slide scanning with 200-slide capacity. This instrument can perform whole-slide fluorescent scanning of up to four fluorophores, including DAPI. It has a standard halogen light source with DAPI, FITC, CY3, Texas Red, CY5 and CY7 filters, which offers imaging with a wide range of fluorophores. It also offers z-stacking, and while z-stacked images are not compatible with HALO or HALO Link, users can view them with Aperio ImageScope. Final images are in the .scn file format.

Akoya Vectra 3

Our Akoya (formerly Perkin Elmer) Vectra 3 automated quantitative pathology imaging system offers high-throughput 20X and 40X multispectral fluorescent imaging with 200-slide capacity. The Vectra 3 has filters for DAPI, FITC, CY3, Texas Red and CY5. Users can select areas of interest using Phenoptics Phenochart on the raw images, and then spectrally unmix these areas with Inform software to isolate and image up to seven-color images (six unique markers plus DAPI nuclear staining). Final images are multilayered .tif files.

Akoya Vectra Polaris

Our Polaris automated quantitative pathology imaging system offers high-throughput 20x and 40x multispectral fluorescent imaging with 80-slide capacity. It has two sets of filters: one set of traditional long-pass filters for DAPI, FITC, CY3, Texas Red and CY5 plus a set of short-pass filters intended for use with Opal fluorescent dyes. Users can perform whole-slide imaging for up to seven-color multispectral images (six markers + DAPI) using the MOTiF workflow, or select areas of interest to image up to nine-color images (eight unique markers plus DAPI nuclear staining). This instrument uses Phenoptics Phenochart and Inform software to process and unmix the raw images. Final images are multilayer .tif or .qptiff files.

Questions about our digital pathology services or how to schedule with us?