This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

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3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

Quantitative Phyletics and the Evolution of Anurans

Mechanism of Activation of the Raf-Erk Signaling Pathway by Oncogenic Mutations of B-Raf

A major developmental transition in early xenopus embryos: I. characterization and timing of cellular changes at the midblastula stage

Despite 100 years of evidence showing a pivotal role for indole-3-acetic acid (IAA or auxin) in plant development, the mechanism of auxin perception has remained elusive. Central to auxin response are changes in gene expression, brought about by auxin-induced interaction between the Aux/IAA transcriptional repressor proteins and the ubiquitin–ligase complex SCFTIR1, thus targeting for them proteolysis. Regulated SCF-mediated protein degradation is a widely occurring signal transduction mechanism. Target specificity is conferred by the F-box protein subunit of the SCF (TIR1 in the case of Aux/IAAs) and there are multiple F-box protein genes in all eukaryotic genomes examined so far. Although SCF–target interaction is usually regulated by signal-induced modification of the target, we have previously shown that auxin signalling involves the modification of SCFTIR1. Here we show that this modification involves the direct binding of auxin to TIR1 and thus that TIR1 is an auxin receptor mediating transcriptional responses to auxin.

The Arabidopsis F-box protein TIR1 is an auxin receptor

Normal Table of Xenopus Laevis (Daudin)

A Systematical and Chronological Survey of the Development from the Fertilized Egg till the End of Metomorphosis

Normal table of Xenopus laevis (Daudin). A systematical and chronological survey of the development from the fertilized egg till the end of metamorphosis.

(DAUDIN). Edited by P. D. Nieuwkoop and J. Faber. North-Holland Publishing Co., Amsterdam. 1956: 243 pp., 10 pls. $6.00.-This is an excellent short but remarkably complete summary of the embryology of this African frog that has become a laboratory animal. Though initiated and edited at the Hubrecht Laboratory of Utrecht, Holland, it has involved the collaboration of 20 distinguished scientists on three continents. A short chapter by H. W. Parker recounts the taxonomic history and current classification of the genus. Another chapter is a brief discussion of the ecology of X. laevis, normal and induced spawning and the rearing of tadpoles. The remaining chapters concisely describe first early embryology, then organogenesis and finally list and characterize the stages of normal development. Each stage or organ system is treated by an expert. There is a very useful 44 page bibliography of Anuran development arranged by special topics. REVIEWS AND COMMENTS 65

Pieter D. Nieuwkoop

Papers

Normal Table of Xenopus Laevis (Daudin)

Normal table of Xenopus laevis (Daudin). A systematical and chronological survey of the development from the fertilized egg till the end of metamorphosis.

Normal table of Xenopus laevis.

Primordial germ cells in the chordates

Primordial germ cells in the chordates : embryogenesis and phylogenesis