Indica Labs ISH-IHC measures one IHC stain and up to two chromogenic and/or silver-labeled DNA or RNA ISH probes on a cell-by-cell basis. This allows the user to rapidly contextualize the corresponding protein and gene expression profile of every cell across the tissue. The HALO ISH-IHC module is designed to work with up to 5 stains, including a nuclear stain and up to 4 IHC biomarkers or ISH probes and supports the H-score protocol for RNAscope as recommended by the manufacturer, ACD, a Bio-techne brand.
The module reports numerous outputs including, but not limited to: number of IHC positive cells in total and by cell compartment, Average IHC OD and average IHC OD by cell compartment, percentage IHC positive total and by cell compartment, number and percentage of probe 1 and/or probe 2 positive cells, probe 1 and probe 2 copies per cell and area per cell, cell score for probe 1 and probe 2 (0, +1, +2, +3 and +4), total H-score for each probe, total cells and percentage of total cells positive for IHC marker and probe 1 and/or probe 2 (dual and triple positive cells). Histograms are automatically generated representing the frequency distribution of probes per cell [Figure 1] and RNAscope cell scoring [Figure 2] as shown below.
Figure 1 shows a distribution curve of probe number on a cell by cell basis, in this example most cells were shown to have between 0-5 copies per cell.
Figure 2. This bar chart shows the numbers of cells that were categorized as 0, 1+, 2+, 3+ and 4+ respectively. The chart shows that a slim majority of cells were positive for RNA probe expression.
The ISH-IHC quantification module integrates seamlessly into the HALO® platform which is compatible with a number of third party systems and file formats.
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
Quantitative RNAscope Image Analysis Guide
Advance your RNAscope image analysis by downloading the latest Quantitative RNAscope Image Analysis Guide from Indica Labs and ACD, a Bio-techne brand.
RNAscope® Publications with the HALO® Image Analysis Platform
Read this publications list to see examples of research in areas from neuroscience to oncology using HALO to analyze RNAscope images.
Publication Spotlight
The table below includes publications that cite the ISH-IHC and FISH-IF modules.
Your publication not on the list? Drop us an email to let us know about it!
| Title | Authors | Year | Journal | Application | HALO Modules | Product |
|---|---|---|---|---|---|---|
| Detection of EpsteinñBarr Virus in Periodontitis: A Review of Methodological Approaches | Tonoyan L, Chevalier M, Vincent-Bungnas S, Marsault R, Doglio A | 2021 | Mircroorganisms | Review | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Detection of engineered T cells in FFPE tissue by multiplex in situ hybridization and immunohistochemistry | Wright JH, Huang L-Y, Weaver S, Archila LD, McAfee MS, Hirayama AV, Chapuis AG, Bleakley M, Rongvaux A, Turtle CJ, Chanthaphavong S, Campbell JS, Pierce RH | 2020 | Journal of Immunological Methods | Immunology | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders | Eroglu E, Yen C, Witman N, Elewa A, Araus A, Wang H, Szattler T, Umeano C, Sohlmer J, Goedel A, Simon A, Chien K | 2022 | Nature Cell Biology | Myology | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype | Porter R, Sun S, Flores M, Berzolla E, You E, Phillips I, KC N, Desai N, Tai E, Szabolcs A, Lang E, Pankaj A, Raabe M, Thapar V, Xu K, Nieman L, Rabe D, Kolin D, Stover E, Pepin D, Stott S, Deshpande V, Liu J, Solovyov A, Matulonis U, Greenbaum B, Ting D | 2022 | The Journal of Clinical Investigation | Immuno-oncology | ISH/FISH, ISH-IHC/FISH-IF | HALO |
| Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density | Somasundaram V, Ridnour L, Cheng R, Walke A, Kedei N, Bhattacharyya D, Wink A, Edmondson E, Butcher D, Warner A, Dorsey T, Scheiblin D, Heinz W, Bryant R, Kinders R, Lipkowitz S, Wong S, Pore M, Hewitt S, McVicar D, Anderson S, Chang J, Glynn S, Ambs S, Lockett S, Wink D | 2022 | Redox Biology | Oncology | Classifer, ISH/FISH, Spatial Analysis, Registration, ISH-IHC/FISH-IF | HALO |
| Annexin A2/TLR2/MYD88 pathway induces arginase 1 expression in tumor-associated neutrophils | Zhang H, Zhu X, Friesen T, Kwak J, Pisarenko T, Mekvanich S, Velasco M, Randolph T, Kargl J, Houghton A | 2022 | Journal of Clinical Investigation | Immuno-oncology | Spatial Analysis, ISH-IHC/FISH-IF | HALO |
| Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarction | Yamada S, Ko T, Hatsuse S, Nomura S, Zhang B, Dai Z, Inoue S, Kubota M, Sawami K, Yamada T, Sassa T, Katagiri M, Fujita K, Katoh M, Ito M, Harada M, Toko H, Takeda N, Morita H, Aburatani H, Komuro I | 2022 | Nature Cardiovascular Research | Myology | ISH-IHC/FISH-IF | HALO |
| Loss of functional System x-c uncouples aberrant postnatal neurogenesis from epileptogenesis in the hippocampus of Kcna1-KO mice | Aloi M, Thompson S, Quartapella N, Noebels J | 2022 | Cell Reports | Neuroscience | ISH-IHC/FISH-IF | HALO |
| Multiparameter immunohistochemistry analysis of HIV DNA, RNA and immune checkpoints in lymph node tissue | Richardson Z, Deleage C, Tutuka C, Walkiewica M, Del Rio-Estrada P, Pascoe R, Evans V, Reyesteran G, Gonzales M, Roberts-Thomson S, Gonzalez-Navarro M, Torres-Ruiz, F, Estes J, Lewin S, Cameron P | 2021 | Journal of Immunological Methods | Infectious Disease | ISH-IHC/FISH-IF | HALO |
| The potassium channel auxiliary subunit Kv_2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing | Yee J, Rastani A, Soden M | 2022 | Journal of Neurophysiology | Neuroscience | ISH-IHC/FISH-IF | HALO |
| Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s disease | Matsushima A, Pineda S, Crittenden J, Lee H, Galani K, Mantero J, Tombaugh G, Kellis M, Heiman M, Graybiel A | 2023 | Nature Communications | Neuroscience | Area Quantification, ISH-IHC/FISH-IF | HALO |
| Exploration of spatial heterogeneity of tumor microenvironment in nasopharyngeal carcinoma via transcriptional digital spatial profiling | Wang L, Wang D, Zeng X, Zhang Q, Wu H, Liu J, Wang Y, Liu G, Poan Y | 2023 | International Journal of Biological Sciences | Oncology | Area Quantification, ISH-IHC/FISH-IF | HALO |
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