Abstract
The Cancer Genome Atlas (TCGA) provides a rich repository of whole mount tumor sections that are collected from different laboratories. However, there are a significant amount of technical and biological variations that impede analysis. We have developed a novel approach for nuclear segmentation in histology sections, which addresses the problem of technical and biological variations by incorporating information from manually annotated reference patches with the local color space of the original image. Subsequently, the problem is formulated within a multi-reference graph cut with geodesic constraints. This approach has been validated on manually curated samples and then applied to a dataset of 440 whole mount tissue sections, originating from different laboratories, which are typically 40k-by-40k pixels or larger. Segmentation results, through a zoomable interface, and extracted morphometric data are available at: http://tcga.lbl.gov.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings - International Symposium on Biomedical Imaging |
| Pages | 856-859 |
| Number of pages | 4 |
| DOIs | |
| State | Published - 2012 |
| Event | 2012 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012 - Barcelona, Spain Duration: May 2 2012 → May 5 2012 |
Other
| Other | 2012 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012 |
|---|---|
| Country | Spain |
| City | Barcelona |
| Period | 5/2/12 → 5/5/12 |
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Keywords
- H&E tissue section
- Nuclear segmentation
- Nuclear/Background classification
ASJC Scopus subject areas
- Biomedical Engineering
- Radiology Nuclear Medicine and imaging
Cite this
Batch-invariant nuclear segmentation in whole mount histology sections. / Chang, Hang; Loss, Leandro A.; Spellman, Paul T.; Borowsky, Alexander D; Parvin, Bahram.
Proceedings - International Symposium on Biomedical Imaging. 2012. p. 856-859 6235683.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Batch-invariant nuclear segmentation in whole mount histology sections
AU - Chang, Hang
AU - Loss, Leandro A.
AU - Spellman, Paul T.
AU - Borowsky, Alexander D
AU - Parvin, Bahram
PY - 2012
Y1 - 2012
N2 - The Cancer Genome Atlas (TCGA) provides a rich repository of whole mount tumor sections that are collected from different laboratories. However, there are a significant amount of technical and biological variations that impede analysis. We have developed a novel approach for nuclear segmentation in histology sections, which addresses the problem of technical and biological variations by incorporating information from manually annotated reference patches with the local color space of the original image. Subsequently, the problem is formulated within a multi-reference graph cut with geodesic constraints. This approach has been validated on manually curated samples and then applied to a dataset of 440 whole mount tissue sections, originating from different laboratories, which are typically 40k-by-40k pixels or larger. Segmentation results, through a zoomable interface, and extracted morphometric data are available at: http://tcga.lbl.gov.
AB - The Cancer Genome Atlas (TCGA) provides a rich repository of whole mount tumor sections that are collected from different laboratories. However, there are a significant amount of technical and biological variations that impede analysis. We have developed a novel approach for nuclear segmentation in histology sections, which addresses the problem of technical and biological variations by incorporating information from manually annotated reference patches with the local color space of the original image. Subsequently, the problem is formulated within a multi-reference graph cut with geodesic constraints. This approach has been validated on manually curated samples and then applied to a dataset of 440 whole mount tissue sections, originating from different laboratories, which are typically 40k-by-40k pixels or larger. Segmentation results, through a zoomable interface, and extracted morphometric data are available at: http://tcga.lbl.gov.
KW - H&E tissue section
KW - Nuclear segmentation
KW - Nuclear/Background classification
UR - http://www.scopus.com/inward/record.url?scp=84864856917&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84864856917&partnerID=8YFLogxK
U2 - 10.1109/ISBI.2012.6235683
DO - 10.1109/ISBI.2012.6235683
M3 - Conference contribution
AN - SCOPUS:84864856917
SN - 9781457718588
SP - 856
EP - 859
BT - Proceedings - International Symposium on Biomedical Imaging
ER -