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).
File formats supported by the HALO image analysis platform:
- Non-proprietary (JPG, TIF, OME.TIFF)
- Nikon (ND2)
- 3D Histech (MRXS)
- Akoya (QPTIFF, component TIFF)
- Olympus / Evident (VSI)
- Hamamatsu (NDPI, NDPIS)
- Aperio (SVS, AFI)
- Zeiss (CZI)
- Leica (SCN, LIF)
- Ventana (BIF)
- Philips (iSyntax, i2Syntax)
- KFBIO (KFB, KFBF)
- DICOM (DCM*)
*whole-slide images
Sequential Same Slide Multiplex IF and H&E Staining for Combined Phenotypic and Morphological Characterization of FFPE Tissue Sections
Read this eBook for an introduction to a sequential staining and image analysis workflow that leverages a terminal H&E stain for the delineation of tissue architectural regions in subsequent HALO image analysis.
Introduction of a Robust Workflow for the Whole-Slide Acquisition and Co-Registration of Multiplex Immunofluorescence Tissue Images for Analysis of a 9-Color, 8-Marker Immunophenotyping Assay
Download our eBook to learn about a HALO workflow for co-registration and cellular analysis of immunofluorescence images from cyclically stained and imaged slides.
Publication Spotlight
The table below includes publications that cite the Serial Section Analysis Add-on.
Your publication not on the list? Drop us an email to let us know about it!
| Title | Authors | Year | Journal | Application | HALO Modules | |
|---|---|---|---|---|---|---|
| A Cdh3-β-catenin-laminin signaling axis in a subset of breast tumor leader cells control leader cell polarization and directional collective migration | Hwang P, Mathur J, Cao Y, Almeida J, Ye J, Morikis V, Cornish D, Clarke M, Stewart S, Pathak A, Longmore G | 2023 | Developmental Cell | Oncology | Highplex FL, Registration | HALO |
| Standardized pathology screening of mature Tertiary Lymphoid Structures in cancers | Vanhersecke L, Bougouin A, Crombe A, Brunet M, Sofeu C, Parrens M, Pierron H, Bonhomme B, Lembege N, Rey C, Velasco V, Soubeyran I, Begueret H, Bessede A, Bellera C, Scoazec J-Y, Italiano A, Fridman C, Fridman W, Le Loarer F | 2023 | Laboratory Investigation | Other | Highplex FL, Registration | HALO |
| Fucosylation of HLA-DRB1 regulates CD4+ T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy | Lester D, Burton C, Gardner A, Innamarato P, Kodumudi K, Liu Q, Adhikari E, Ming Q, Williamson D, Frederick D, Sharova T, White M, Markowitz J, Cao B, Nguyen J, Johnson J, Beatty M, Mockabee-Macias A, Mercurio M, Watson G, Chen P-L, McCarthy S, MoranSegura C, Messina J, Thomas K, Darville L, Izumi V, Koomen J, Pilon-Thomas S, Ruffell B, Luca V, Haltiwanger R, Wang X, Wargo J, Boland G, Lau E | 2023 | Nature Cancer | Immuno-oncology | Highplex FL, Registration | HALO |
| CXCL9 and CXCL13 coordinately shape the immune-activated microenvironment of endometrial cancer via tertiary lymphoid structure formation | Kodama M, Nagase Y, Aimono E, Nakamura K, Takamatsu R, Abe K, Yoshimura T, Chiyoda T, Yamagami W, Aoki D, Nishihara H | 2023 | Research Square | Immuno-oncology | Registration | HALO |
| African-Ancestry Associated Gene Expression Signatures and Pathways in Triple Negative Breast Cancer, a Comparison across Women of African Descent | Martini R, Delpe P, Chu T, Arora K, Lord B, Verma A, Chen Y, Gebregzabher, Oppong J, Adjei E, Jibril A, Awuah B, Bekele M, Abebe E, Kyei I, Aitpillah F, Adinku M, Ankomah K, Osei-Bonsu E, Chitale D, Bensenhaver J, Nathanson S, Jackson L, Jiagge E, Petersen L, Proctor E, Gyan K, Gibbs L, Monojlovic Z, Kittles R, White J, Yates C, Manne U, Gardner K, Mongan N, Cheng E, Ginter P, Hoda S, Elemento O, Robine N, Sboner A, Carpten J, Newman L, Davis M | 2022 | medRxiv | Oncology | Multiplex IHC, Serial Section | |
| Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate Cancer | Ozbek B, Ertunc O, Erickson A, Vidal I, Gomes-Alexandre C, Guner G, Hicks J, Jones T, Taube J, Sfanos K, Yegnasubramanian S, DeMarzo A | 2022 | The Prostate | Immuno-oncology | Classifier, Cytonuclear, Highplex FL, Serial Section, Registration, Figure Maker, TMA | |
| 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 images | Ono 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 T | 2020 | Cancer Medicine | Classifier, Multiplex IHC, Serial Section | ||
| Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancers | Chalabi 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 JB | 2020 | Nature Medicine | Immuno-oncology | Multiplex 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 JM | 2018 | Journal for ImmunoTherapy of Cancer | Oncology, Immuno-oncology | Spatial Analysis, Serial Section |
Related HALO Modules
Separate multiple tissue classes across a tissue using a learn-by-example approach. Can be used in conjunction with all other modules (fluorescent and brightfield) to select specific tissue classes for further analysis.
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Plot cells and objects from one or more images and perform nearest neighbor analysis, proximity analysis, and tumor infiltration analysis.
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Quantify expression of up to five brightfield stains in any cellular compartment - membrane, nucleus or cytoplasm.
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