Object classification does not alter the precision or accuracy of segmentation by AIVE. (A–E) Flow chart depicting object classification during AIVE, in which (A) organelle labels and (B) membrane predictions are multiplied to generate (C) a contextually masked membrane prediction, (D) which is then combined with the normalized EM data to generate (E) AIVE data belonging to a specific organelle. (F) 2D examples of mitochondrial classification labels provided by one human on different days or two 3D U-Nets with different initialization seeds. (G–J) 3D-rendered results classified using the labels shown in Fig. 3 F, after classification via (G) conventional instance segmentation or by using the binary labels (H) for selective VE, (I) AIE, or (J) AIVE. (K–M) Quantitative analysis of (K) the distance between mitochondrial membranes and each mitochondrial 3D probe (probe locations shown in Fig. S1 D; also see Video 2 for rotation animation depicting probe positions), (L) the range of values recorded by each 3D probe, and (M) the relative absolute deviation in 3D probe measurements for all datasets shown in Fig. 3, H–J. (N–P) 2D maximum intensity projections of 18 individual nuclear pores, which were spatially aligned prior to processing and segmentation via (N) VE, (O) AIE, or (P) AIVE (unprocessed pores are shown, and pore locations are shown in Fig. S1, E and F, respectively). (Q) Feret’s diameter measurements of the central transport channel from each nuclear pore after segmentation via VE, AI, or AIVE (black arrowhead indicates diameter reported by Schuller et al. (2021); hollow arrowhead range indicates diameters reported by Zimmerli et al. (2021). (R–T) 2D projections and 3D renderings showing the median averaged data generated via (Q) VE, (R) AI, or (S) AIVE (purple), with spatial alignment to the NPC structure (orange) published in 2021 by Schuller et al. (2021). Plot markers in K–L indicate values for individual 3D probes. Plot markers in T indicate measurements for individual nuclear pores. The interquartile range is indicated by the box, median is indicated by the horizontal lines, and the minimum and maximum are indicated by whiskers. Scale bars; A–J, 200 nm; N–S, 100 nm.
Figure 3.

Object classification does not alter the precision or accuracy of segmentation by AIVE. (A–E) Flow chart depicting object classification during AIVE, in which (A) organelle labels and (B) membrane predictions are multiplied to generate (C) a contextually masked membrane prediction, (D) which is then combined with the normalized EM data to generate (E) AIVE data belonging to a specific organelle. (F) 2D examples of mitochondrial classification labels provided by one human on different days or two 3D U-Nets with different initialization seeds. (G–J) 3D-rendered results classified using the labels shown in Fig. 3 F, after classification via (G) conventional instance segmentation or by using the binary labels (H) for selective VE, (I) AIE, or (J) AIVE. (K–M) Quantitative analysis of (K) the distance between mitochondrial membranes and each mitochondrial 3D probe (probe locations shown in Fig. S1 D; also see Video 2 for rotation animation depicting probe positions), (L) the range of values recorded by each 3D probe, and (M) the relative absolute deviation in 3D probe measurements for all datasets shown in Fig. 3, H–J. (N–P) 2D maximum intensity projections of 18 individual nuclear pores, which were spatially aligned prior to processing and segmentation via (N) VE, (O) AIE, or (P) AIVE (unprocessed pores are shown, and pore locations are shown in Fig. S1, E and F, respectively). (Q) Feret’s diameter measurements of the central transport channel from each nuclear pore after segmentation via VE, AI, or AIVE (black arrowhead indicates diameter reported by Schuller et al. (2021); hollow arrowhead range indicates diameters reported by Zimmerli et al. (2021). (R–T) 2D projections and 3D renderings showing the median averaged data generated via (Q) VE, (R) AI, or (S) AIVE (purple), with spatial alignment to the NPC structure (orange) published in 2021 by Schuller et al. (2021). Plot markers in K–L indicate values for individual 3D probes. Plot markers in T indicate measurements for individual nuclear pores. The interquartile range is indicated by the box, median is indicated by the horizontal lines, and the minimum and maximum are indicated by whiskers. Scale bars; A–J, 200 nm; N–S, 100 nm.

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