Benchmark for multi-cellular segmentation of bright field microscopy images

BMC Bioinformatics

Assaf Zaritsky³  Nathan Manor³  Lior Wolf³  Eshel Ben-Jacob¹  Ilan Tsarfaty² 

[1] Research & Development Unit Assaf Harofeh Medical Center, Zerifin, 70300, Israel

[2] Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel

[3] Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel

关键词: Benchmarking;    Segmentation;    Wound healing assay;    Collective cell migration;   

Others  :  1087718
DOI  :  10.1186/1471-2105-14-319

 received in 2013-06-20, accepted in 2013-10-29,  发布年份 2013

【 摘 要 】

Background

Multi-cellular segmentation of bright field microscopy images is an essential computational step when quantifying collective migration of cells in vitro. Despite the availability of various tools and algorithms, no publicly available benchmark has been proposed for evaluation and comparison between the different alternatives.

Description

A uniform framework is presented to benchmark algorithms for multi-cellular segmentation in bright field microscopy images. A freely available set of 171 manually segmented images from diverse origins was partitioned into 8 datasets and evaluated on three leading designated tools.

Conclusions

The presented benchmark resource for evaluating segmentation algorithms of bright field images is the first public annotated dataset for this purpose. This annotated dataset of diverse examples allows fair evaluations and comparisons of future segmentation methods. Scientists are encouraged to assess new algorithms on this benchmark, and to contribute additional annotated datasets.

【 授权许可】

   
2013 Zaritsky et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Simpson KJ, Selfors LM, Bui J, Reynolds A, Leake D, Khvorova A, Brugge JS: Identification of genes that regulate epithelial cell migration using an siRNA screening approach. Nat Cell Biol 2008, 10(9):1027-1038.
• [2]Petitjean L, Reffay M, Grasland-Mongrain E, Poujade M, Ladoux B, Buguin A, Silberzan P: Velocity fields in a collectively migrating epithelium. Biophys J 2010, 98(9):1790-1800.
• [3]Peruani F, Starruss J, Jakovljevic V, Sogaard-Andersen L, Deutsch A, Bar M: Collective motion and nonequilibrium cluster formation in colonies of gliding bacteria. Phys Rev Lett 2012, 108(9):098102.
• [4]Deforet M, Parrini MC, Petitjean L, Biondini M, Buguin A, Camonis J, Silberzan P: Automated velocity mapping of migrating cell populations (AVeMap). Nat Methods 2012, 9(11):1081-1083.
• [5]Milde F, Franco D, Ferrari A, Kurtcuoglu V, Poulikakos D, Koumoutsakos P: Cell Image Velocimetry (CIV): boosting the automated quantification of cell migration in wound healing assays. Integr Biol 2012, 4(11):1437-1447.
• [6]Geback T, Schulz MM, Koumoutsakos P, Detmar M: TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays. Biotechniques 2009, 46(4):265-274.
• [7]Korzynska A, Strojny W, Hoppe A, Wertheim D, Hoser P: Segmentation of microscope images of living cells. Pattern Anal Appl 2007, 10(4):301-319.
• [8]Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, Yli-Harja O, Aderem A, Shmulevich I: Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. Plos One 2009, 4(10):e7497.
• [9]Ali R, Gooding M, Christlieb M, Brady M: Advanced phase-based segmentation of multiple cells from brightfield microscopy images. In 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro: 2008. Paris: ; 2008:181-184.
• [10]Topman G, Sharabani-Yosef O, Gefen A: A standardized objective method for continuously measuring the kinematics of cultures covering a mechanically damaged site. Med Eng Phys 2011, 34:225-232.
• [11]Zordan MD, Mill CP, Riese DJ, Leary JF: A high throughput, interactive imaging, bright-field wound healing assay. Cytometry A 2011, 79A(3):227-232.
• [12]Placidi G, Sabatini M, Gallucci M, Sotgiu A: A calculation method for semi automatic follow up of multiple sclerosis by magnetic resonance eco planar perfusion imaging. Stud Health Technol Inform 2003, 95:164-169.
• [13]Qin J, Chittenden TW, Gao L, Pearlman JD: Automated migration analysis based on cell texture: method & reliability. BMC Cell Biol 2005, 6(1):9.
• [14]Skopin MD, Molitor SC: Effects of near-infrared laser exposure in a cellular model of wound healing. Photodermatol Photoimmunol Photomed 2009, 25(2):75-80.
• [15]Zaritsky A, Natan S, Horev J, Hecht I, Wolf L, Ben-Jacob E, Tsarfaty I: Cell motility dynamics: a novel segmentation algorithm to quantify multi-cellular bright field microscopy images. Plos One 2011, 6(11):e27593.
• [16]Evanko D: All things being equal. Nat Methods 2012, 9(2):111.
• [17]Treloar KK, Simpson MJ: Sensitivity of edge detection methods for quantifying cell migration assays. PLoS One 2013, 8(6):e67389.
• [18]Smith R, Ventura D, Prince JT: Novel algorithms and the benefits of comparative validation. Bioinformatics 2013, 29(12):1583-1585.
• [19]Liang CC, Park AY, Guan JL: In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro. Nat Protoc 2007, 2(2):329-333.
• [20]Ljosa V, Sokolnicki KL, Carpenter AE: Annotated high-throughput microscopy image sets for validation. Nat Methods 2012, 9(7):637.
• [21]Lampugnani MG: Cell migration into a wounded area in vitro. Methods Mol Biol 1999, 96:177-182.
• [22]Zahm JM, Kaplan H, Herard AL, Doriot F, Pierrot D, Somelette P, Puchelle E: Cell migration and proliferation during the in vitro wound repair of the respiratory epithelium. Cell Motil Cytoskeleton 1997, 37(1):33-43.
• [23]Yarrow JC, Perlman ZE, Westwood NJ, Mitchison TJ: A high-throughput cell migration assay using scratch wound healing, a comparison of image-based readout methods. BMC Biotechnol 2004, 4:21.
• [24]Swedlow JR: Finding an image in a haystack: the case for public image repositories. Nat Cell Biol 2011, 13(3):183.
• [25]Boulesteix AL: On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al. Bioinformatics 2013, 29(20):2664-2666.
• [26]Boulesteix AL, Lauer S, Eugster MJ: A plea for neutral comparison studies in computational sciences. PLoS One 2013, 8(4):e61562.