Indica
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Serial Registration Analysis

co-expression markup serial section analysis

SERIAL REGISTRATION ANALYSIS ADD-ON

 

Product Overview

The Serial Registration Analysis add-on includes options for both serial section analysis and serial stain fusion analysis.

Serial section analysis allows users to create a tissue classifier based off a reference slide (e.g., H&E or Pan-CK) and then apply the resulting classification mask to serial section(s) stained for additional IHC markers (e.g., HER2, ER, PR, Ki-67, CD8, CD4).  In the example above, a tissue biopsy section is stained with hematoxylin and eosin. A classifier has been created segmenting tumor from stroma (Tumor in red, stroma in green, glass in yellow). The serial section add-on takes the Classifier created from the H&E image and allows the user to apply the resulting classification mask to IHC-stained serial sections (e.g., ER, HER2) as regions of interest. The tumor regions, based off of the H&E classifier, are analyzed on the ER and HER2 slides using the Cytonuclear Module and Membrane Module, respectively.  Serial registration analysis is compatible with both brightfield and fluorescent images and any of our HALO modules can be used for the final analysis step.

Where serial section analysis involves different tissue sections that have been stained with different markers, serial stain fusion facilitates analysis of single slides that have been stained, stripped and restained (as described in Romain Remark et al. Science Immunology, 2016).  As demonstrated below, the brightfield images are deconvolved into their composite stains (nuclear counterstain and biomarker stain) and converted to a pseudo-fluorescent images in Step 1. In Step 2, the images are registered using a customizable set of configuration settings. Serial Stain Registration uses an Image Consistency Phase, a Similarity-Only Phase, and a High-Resolution Registration to precisely align single cells. Additionally, a Single Channel Registration option allows the user to align the images using one consistent fluorescent channel, typically DAPI, to improve the registration. Then, the registered serial stain images can be fused into a single composite fluorescent image that can be analyzed using Highplex FL or (any of our other FL modules).

The Serial Registration Analysis add-on integrates seamlessly into the HALO™ platform and is compatible with a number of  file formats.

Contact info@indicalab.com for product demonstration and pricing information or upload some images for a free trial.

SERIAL REGISTRATION ANALYSIS ADD-ON

Serial section analysis allows users to create a tissue classifier based off a reference slide (e.g., H&E or Pan-CK) and then apply the resulting classification mask to serial section(s) stained for additional IHC markers (e.g., HER2, ER, PR, Ki-67, CD8, CD4).  In the example above, a tissue biopsy section is stained with hematoxylin and eosin. A classifier has been created segmenting tumor from stroma (Tumor in red, stroma in green, glass in yellow). The serial section add-on takes the Classifier created from the H&E image and allows the user to apply the resulting classification mask to IHC-stained serial sections (e.g., ER, HER2) as regions of interest. The tumor regions, based off of the H&E classifier, are analyzed on the ER and HER2 slides using the Cytonuclear Module and Membrane Module, respectively.  Serial registration analysis is compatible with both brightfield and fluorescent images and any of our HALO modules can be used for the final analysis step.

Where serial section analysis involves different tissue sections that have been stained with different markers, serial stain fusion facilitates analysis of single slides that have been stained, stripped and restained (as described in Romain Remark et al. Science Immunology, 2016).  As demonstrated below, the brightfield images are deconvolved into their composite stains (nuclear counterstain and biomarker stain) and converted to a pseudo-fluorescent images in Step 1. In Step 2, the images are registered using a customizable set of configuration settings. Serial Stain Registration uses an Image Consistency Phase, a Similarity-Only Phase, and a High-Resolution Registration to precisely align single cells. Additionally, a Single Channel Registration option allows the user to align the images using one consistent fluorescent channel, typically DAPI, to improve the registration. Then, the registered serial stain images can be fused into a single composite fluorescent image that can be analyzed using Highplex FL or (any of our other FL modules).

HALO is compatible with a broad spectrum of image and digital slide formats.  Yours not on the list? Email us your requirements.

Non-proprietary (JPG, TIF)
Nikon (ND2)
3D Histech (MRXS)
Perkin Elmer (QPTIFF, component TIFF)
Olympus (VSI)
Hamamatsu (NDPI, NDPIS)
Aperio (SVS, AFI)
Zeiss (CZI)
Leica (SCN, LIF)
Philips (Requires Philips IMS)

Here are a few publications that cite the use of our Serial Registration Analysis add-on. Your publication not on the list?  Drop us an email to let us know about it!

TitleAuthorsYearJournalApplicationHALO Modules
Assessment of associations between clinical and immune microenvironmental factors and tumor mutation burden in resected nonsmall cell lung cancer by applying machine learning to whole-slide imagesOno A, Terada Y, Kawata T, Serizawa M, Isaka M, Kawabata T, Imai T, Mori K, Muramatsu K, Hayashi I, Kenmotsu H, Oshima K, Urakami K, Nagashima T, Kusuhara M, Akiyama Y, Sugino T, Ohde Y, Yamaguchi K, Takahashi T T2020Cancer MedicineClassifier, Multiplex IHC, Serial Section
Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancersChalabi M, Fanchi LF, Dijkstra KK, Van den Berg JG, Aalbers AG, Sikorska K, Lopez-Yurda M, Grootscholten C, Beets GL, Snaebjornsson P, Maas M, Mertz J, Veninga V, Bounova G, Broeks A, Beets-Tan RG, de Wijkerslooth TR, van Lent AU, Marsman HA, Nuijten E, Kok NF, Kuiper M, Verbeek WH, Kok M, Van Leerdam ME, Schumacher TN, Voest EE, Haanen JB2020Nature MedicineImmuno-oncologyMultiplex IHC, Serial Section
Multidimensional, quantitative assessment of PD-1/PD-L1 expression in patients with Merkel cell carcinoma and association with response to pembrolizumab Giraldo NA, Nguyen P, Engle EL, Kaunitz GJ, Cottrell TR, Berry S, Green B, Soni A, Cuda JD, Stein JE, Sunshine JC, Succaria F, Xu H, Ogurtsova A, Danilova L, Church CD, Miller NJ, Fling S, Lundgren L, Ramchurren N, Yearley JH, Lipson EJ, Cheever M, Anders RA, Nghiem PT, Topalian SL, Taube JM2018Journal for ImmunoTherapy of CancerOncology, Immuno-oncologySpatial Analysis, Serial Section

Use the form below to upload up to three images for us to analyze using HALO.  If the form does not display, please click here.