HistomicsTK

HistomicsTK is an open-source project that provides developers with building blocks for creating pathology image analysis pipelines. It includes functions for preprocessing like color normalization routines, color deconvolution, and color space transformations, functions for nuclei segmentation, and a feature extraction library for computing morphometric features. HistomicsTK also includes a large number of utility functions for working with annotations from the Digital Slide Archive and to prepare results for visualization in DSA.

HistomicsTK can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI and the Digital Slide Archive.

Read more about HistomicsTK here.

Members

Sanghoon Lee, PhD
Postdoctoral Researcher
Mohamed Amgad
PhD Candidate
Lee Cooper, PhD
Principal Investigator

Publications

Mobadersany P, Cooper LA, Goldstein JA. GestAltNet: aggregation and attention to improve deep learning of gestational age from placental whole-slide images. Laboratory Investigation. 2021 Mar 5:1-0.

Amgad M, Elfandy H, Hussein H, Atteya LA, Elsebaie MA, Abo Elnasr LS, Sakr RA, Salem HS, Ismail AF, Saad AM, Ahmed J. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019 Sep 15;35(18):3461-7.

Chandrasekaran S, Sasaki M, Scharer CD, Kissick HT, Patterson DG, Magliocca KR, Seykora JT, Sapkota B, Gutman DA, Cooper LA, Lesinski GB. Phosphoinositide 3-kinase signaling can modulate MHC class I and II expression. Molecular Cancer Research. 2019 Dec 1;17(12):2395-409.

Chittajallu DR, Siekierski N, Lee S, Gerber S, Beezley J, Manthey D, Gutman D, Cooper LAD. Vectorized persistent homology representations for characterizing glandular architecture in histology images. In 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) 2018 Apr 4 (pp. 232-235).

Gutman DA, Khalilia M, Lee S, Nalisnik M, Mullen Z, Beezley J, Chittajallu DR, Manthey D, Cooper LA. The digital slide archive: A software platform for management, integration, and analysis of histology for cancer research. Cancer research. 2017 Nov 1;77(21):e75-8.

Lazar AJ, McLellan MD, Bailey MH, Miller CA, Appelbaum EL, Cordes MG, Fronick CC, Fulton LA, Fulton RS, Mardis ER, Schmidt HK. Comprehensive and integrated genomic characterization of adult soft tissue sarcomas. Cell. 2017 Nov 2;171(4):950-65.

M Ceccarelli, FP Barthel, TM Malta, TS Sabedot, SR Salama, SM Pagnotta, BA Murray, O Mo- rozova, Y Newton, J Wang, DJ Brat, P Zoppoli, R Akbani, AD Cherniack, H Zhang, L Posson, T Mikelsen, WKA Yung, J Huse, CC Lau, A Rao, M Grifford, M Wrensch, R Beroukhim, LAD Cooper, R Rabadan, KD Aldape, PW Laird, DH Gutmann, H Noushmehr, A Iavarone, RGW Verhaak, The Cancer Genome Atlas Research Network, Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell. 2016 Jan 28;164(3):550-63.

Funding

Advanced Development of an Open-Source Platform for Web-Based Integrative Digital Image Analysis in Cancer
NCI U24CA194362
$4,501,083
Informatics Tools for Quantitative Digital Pathology Profiling and Integrated Prognostic Modeling
NCI U01CA220401
$1,613,071