Fig. 5: Instantiation of the framework with recommendations for concrete biomedical questions.

From top to bottom: (1) Image classification for the examples of sperm motility classification⁶² and disease classification in dermoscopic images^63,58. (2) SemS of large objects for the examples of embryo segmentation from microscopy⁶⁴ and liver segmentation in CT images^65,66. (3) Detection of multiple and arbitrarily located objects for the examples of cell detection and tracking during the autophagy process^67,68 and MS lesion detection in multimodal brain MRI images^69,70. (4) InS of tubular objects for the examples of InS of neurons from the fruit fly^71,72,73 and surgical instrument InS⁶¹. The corresponding traversals through the decision trees are shown in Supplementary Note 4. An overview of the recommended metrics can be found in Supplementary Note 3.1, including relevant information for each metric. ImLC-2, reproduced from dermoscopedia under a Creative Commons license CC BY 4.0; SemS-2, reproduced with permission from ref. ⁶⁵, Springer Nature Limited; InS-1, reproduced with permission from ref. ⁶¹, Springer Nature Limited.