IHC Small Intestine - Dots
Segment nuclei and villi, detect single dot markers (CISH/RNAscope/SISH) in villi and manually defined crypts, and quantify dot count, area, intensity, and distribution per region.
metastructures
single-cell analysis
dot detection
small intestine, crypts, villi, RNAScope, CISH
The IHC Small Intestine - Dots App provides nuclei segmentation as well as detection of tissue and villi based on nuclei staining. crypts need to be defined manually. Furthermore it allows the dot detection for one dot markers (CISH, RNAScope, SISH) within villi and crypt area. Dot parameters are provided for villi and crypts and include count, mean intensity, total dot area, and sum of intensity as well as area and intensity lists for all single dots.
Image courtesy of Emma Nye, Head of Experimental Histopathology, The Francis Crick Institute, London, UK
Original Image
Villi detection
Crypt detection
Villi and dot detection
dot detection
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15 Feb, 2023
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single-cell analysis
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30 Mar, 2026
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metastructures
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We support the following file formats:
- TissueFAXS (aqproj)
- StrataFAXS II (vmic)
- PreciPoint (vmic, gtif)
- Generic BigTIFF Import
- Support for multipage BigTIFF files
- OME-TIFF
- JPEG, PNG, BMP, TIFF
- Zeiss (czi)
- Hamamatsu NanoZoomer (ndpi)
- Aperio (svs)
- Leica (scn)
- 3D HISTECH Pannoramic
- Mirax (mrxs)
- Olympus (vsi)
- More slide scanners to be added!
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Perfectly tailored image analysis solutions for your research.
You have a specific research question that needs to be answered? We offer custom development of image analysis pipelines for specific tasks, be it detection of cellular phenotypes or quantification of tissue structures. After discussing your goals with one of our experts, you will get a ready-to-use App and be a step closer to an impactful publication.
