Figure 5
Qualitative comparison of 3D U-Net membrane reconstructions using TM or AMST aligned datasets (subsets from aligned HeLa dataset, EMPIAR-10311). (a) Raw data slice of the test set. (b,c) Membrane reconstructions of the same slice from TM and AMST aligned datasets, respectively. Red and green arrows indicate organelle boundaries that were substantially improved upon alignment with AMST. (d,e) 3D renderings of a sub-volume containing the predictions shown in (b,c), respectively. Membrane reconstruction quality was substantially improved when using AMST aligned data. Jumps in the data alignment as found in the TM dataset, frequently disrupted the membrane prediction and thus membrane connectivities. The 3D renderings were oriented such that a stretch of the plasma membrane is visible in the front. The orange arrow heads (b–e) point to the same location in identical direction parallel to the image slices. The yellow arrows highlight the plasma membrane, magenta arrows an ER sheet.
