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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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:
5TC_1 multiplex panel on tonsil
GFP_Inf5 multiplex panel on gut
7TME-1 multiplex panel on tonsil
5TC_1 multiplex panel on tonsil
GFP_Inf5 multiplex panel on gut
7TME-1 multiplex panel on tonsil
The HALO image analysis software processes both chromogenic and fluorescent images from multiple imaging platforms. Users can fuse single-channel images and tiles, while also allowing registration and overlay of parallel images for concurrent analysis. Users can enhance their analysis by annotating distinct layers within images, or developing classifiers to define regions of interest based on distinct colors or textures.
For quantitative analysis, HALO offers both gross area measurements and cell counting via nuclear detection. AI capabilities are available as an option to improve nuclear segmentation and machine learning-based classification of unique regions. Analysis results can be viewed as either summary data or cell-by-cell object data, which can be exported to Excel for further analysis. Additionally, users can perform spatial/proximity analysis directly within HALO.
The following image analysis modules are available for use on the HALO workstations:
- HALO AI
- 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)
HALO software training is available by our expert staff. Further learning tools are available through the Indica Labs online Learning Portal , which features tutorial videos, webinars, user guides, and technical documentation. We also offer fee-based expert assistance and image analysis services.
VisioPharm Image Analysis software can perform quantitative image analysis from a variety of imaging platforms. Phenoplex, AI, Tissue Align, Tissuearray, apps, training or Exp Histo analysis, or a combination of both (Exp Histo develops app for thresholding by user).
Our Evident VS200 and Aperio VERSA 200 systems perform brightfield imaging on standard 75mm x 25mm microscope slides at magnifications from 20X to 63X (dry), using external illumination to capture specimens against a uniformly lit background. These same systems, along with our Akoya PhenoImager HT, also support multiplex fluorescent imaging. The VS200 and VERSA 200 can detect up to three markers, plus DAPI nuclear counterstain, and are available for hourly rental and training. For more complex studies, our imaging services using the PhenoImager HT can detect up to eight unique markers plus nuclear counterstain.
For users who are unable to access our HALO Link image management software, Aperio files may be viewed in Aperio ImageScope and Evident VS200 files may be viewed using the Evident OlyVIA free downloadable software for Windows OS.
We offer training for the independent use of the following instruments/software, in addition to providing these services for a fee. Please contact exphisto@fredhutch.org to schedule customized one-on-one training.
- Leica LMD6 Laser Capture Microdissection microscope
- Evident VS200
- Aperio Versa fluorescent slide scanner
- HALO Image Analysis softare
- VisioPharm image analysis software
Additional training resources for HALO are available through their online Learning Portal, including tutorial videos, webinars, user guides, and technical documentation. For VisioPharm support materials, please visit their dedicated support portal.
Our core maintains two VS200 digital pathology slide scanners with distinct configurations. The first scanner, operated by EH staff, specializes in high throughput brightfield imaging at 20X or 40X magnification, delivering high-quality images with rapid turnaround. Images are uploaded to HALO Link for convenient access and collaboration, unless requested otherwise.
The second VS200 instrument is available for both investigator training and independent use at an hourly rate, as well as for EH staff operations. This six-slide capacity instrument offers versatile imaging options, including brightfield, polarized light and fluorescent imaging with standard filter sets (DAPI, FITC, TRITC, Texas Red and CY5). It features manual focusing abilities for challenging samples and supports Z-stack images with post-processing options for extended focal imaging (EFI) or deconvolution. All images are saved in .vsi format.
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.
Our Akoya PhenoImager HT 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.