A quantitative metric for the comparative evaluation of optical clearing protocols for 3D multicellular spheroids

3D multicellular spheroids quickly emerged as in vitro models because they represent the in vivo tumor environment better than standard 2D cell cultures. However, with current microscopy technologies, it is difficult to visualize individual cells in the deeper layers of 3D samples mainly because of limited light penetration and scattering. To overcome this problem several optical clearing methods have been proposed but defining the most appropriate clearing approach is an open issue due to the lack of a gold standard metric. Here, we propose a guideline for 3D light microscopy imaging to achieve single-cell resolution. The guideline includes a validation experiment focusing on five optical clearing protocols. We review and compare seven quality metrics which quantitatively characterize the imaging quality of spheroids. As a test environment, we have created and shared a large 3D dataset including approximately hundred fluorescently stained and optically cleared spheroids. Based on the results we introduce the use of a novel quality metric as a promising method to serve as a gold standard, applicable to compare optical clearing protocols, and decide on the most suitable one for a particular experiment

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

aSummary: 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 and embryos) show that the precision of the segmentation reaches the level of a human expert.Peer reviewe

MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility. © 2021, The Author(s)

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

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

MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

none51siSpheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.openPeirsman A.; Blondeel E.; Ahmed T.; Anckaert J.; Audenaert D.; Boterberg T.; Buzas K.; Carragher N.; Castellani G.; Castro F.; Dangles-Marie V.; Dawson J.; De Tullio P.; De Vlieghere E.; Dedeyne S.; Depypere H.; Diosdi A.; Dmitriev R.I.; Dolznig H.; Fischer S.; Gespach C.; Goossens V.; Heino J.; Hendrix A.; Horvath P.; Kunz-Schughart L.A.; Maes S.; Mangodt C.; Mestdagh P.; Michlikova S.; Oliveira M.J.; Pampaloni F.; Piccinini F.; Pinheiro C.; Rahn J.; Robbins S.M.; Siljamaki E.; Steigemann P.; Sys G.; Takayama S.; Tesei A.; Tulkens J.; Van Waeyenberge M.; Vandesompele J.; Wagemans G.; Weindorfer C.; Yigit N.; Zablowsky N.; Zanoni M.; Blondeel P.; De Wever O.Peirsman A.; Blondeel E.; Ahmed T.; Anckaert J.; Audenaert D.; Boterberg T.; Buzas K.; Carragher N.; Castellani G.; Castro F.; Dangles-Marie V.; Dawson J.; De Tullio P.; De Vlieghere E.; Dedeyne S.; Depypere H.; Diosdi A.; Dmitriev R.I.; Dolznig H.; Fischer S.; Gespach C.; Goossens V.; Heino J.; Hendrix A.; Horvath P.; Kunz-Schughart L.A.; Maes S.; Mangodt C.; Mestdagh P.; Michlikova S.; Oliveira M.J.; Pampaloni F.; Piccinini F.; Pinheiro C.; Rahn J.; Robbins S.M.; Siljamaki E.; Steigemann P.; Sys G.; Takayama S.; Tesei A.; Tulkens J.; Van Waeyenberge M.; Vandesompele J.; Wagemans G.; Weindorfer C.; Yigit N.; Zablowsky N.; Zanoni M.; Blondeel P.; De Wever O