Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids, embryos) show that the precision of the segmentation reaches the level of a human expert.

3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images / Tasnadi E.A.; Toth T.; Kovacs M.; Diosdi A.; Pampaloni F.; Molnar J.; Piccinini F.; Horvath P.. - In: BIOINFORMATICS. - ISSN 1367-4811. - ELETTRONICO. - 36:9(2020), pp. 2948-2949. [10.1093/bioinformatics/btaa029]

3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images

Piccinini F.;
2020

Abstract

Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids, embryos) show that the precision of the segmentation reaches the level of a human expert.
2020
3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images / Tasnadi E.A.; Toth T.; Kovacs M.; Diosdi A.; Pampaloni F.; Molnar J.; Piccinini F.; Horvath P.. - In: BIOINFORMATICS. - ISSN 1367-4811. - ELETTRONICO. - 36:9(2020), pp. 2948-2949. [10.1093/bioinformatics/btaa029]
Tasnadi E.A.; Toth T.; Kovacs M.; Diosdi A.; Pampaloni F.; Molnar J.; Piccinini F.; Horvath P.
File in questo prodotto:
File Dimensione Formato  
0050_2020_BioInformatics_Tasnadi.pdf

accesso aperto

Tipo: Versione (PDF) editoriale
Licenza: Licenza per Accesso Aperto. Creative Commons Attribuzione - Non commerciale (CCBYNC)
Dimensione 269.8 kB
Formato Adobe PDF
269.8 kB Adobe PDF Visualizza/Apri
btaa029_supplementary_data.pdf

accesso aperto

Tipo: File Supplementare
Licenza: Licenza per Accesso Aperto. Creative Commons Attribuzione - Non commerciale (CCBYNC)
Dimensione 952.11 kB
Formato Adobe PDF
952.11 kB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/762189
Citazioni
  • ???jsp.display-item.citation.pmc??? 10
  • Scopus 12
  • ???jsp.display-item.citation.isi??? 11
social impact