2014
DOI: 10.1242/dev.108720
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Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience

Abstract: A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new 'a… Show more

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Cited by 40 publications
(48 citation statements)
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“…At this stage, the nervous system and locomotor apparatus is largely differentiated and fully functional. So far, in other animal models similar cellular resolution expression atlases exist for selected tissues only (29,30). Building on previous image registration approaches (25,26), ProSPr is a highly automated and easy-to-customize technique, running in free license software (Scripts available in prospr.embl.…”
Section: Discussion Cellular-resolution Expression Atlases For Complementioning
confidence: 99%
“…At this stage, the nervous system and locomotor apparatus is largely differentiated and fully functional. So far, in other animal models similar cellular resolution expression atlases exist for selected tissues only (29,30). Building on previous image registration approaches (25,26), ProSPr is a highly automated and easy-to-customize technique, running in free license software (Scripts available in prospr.embl.…”
Section: Discussion Cellular-resolution Expression Atlases For Complementioning
confidence: 99%
“…The segmented larva has ~30 bilateral body wall muscles per segment and a similar number of motor neurons, and their role during larval locomotion has been characterized (Berni et al, 2012; Crisp et al, 2008; Crisp et al, 2011; Dixit et al, 2008; Heckscher et al, 2012; Hughes and Thomas, 2007; Lahiri et al, 2011; Pulver and Griffith, 2010; Schaefer et al, 2010). In contrast, there are ~270 bilateral interneurons per segment (Heckscher et al, 2014; Rickert et al, 2011) and their role in locomotion is almost completely unknown (Kohsaka et al, 2014). Recently, we identified several hundred Gal4 lines that express in a sparse pattern of neurons in the late embryonic CNS, and determined their expression pattern at single neuron resolution for 75 of these lines (Heckscher et al, 2014; Manning et al, 2012).…”
Section: Introductionmentioning
confidence: 99%
“…In contrast, there are ~270 bilateral interneurons per segment (Heckscher et al, 2014; Rickert et al, 2011) and their role in locomotion is almost completely unknown (Kohsaka et al, 2014). Recently, we identified several hundred Gal4 lines that express in a sparse pattern of neurons in the late embryonic CNS, and determined their expression pattern at single neuron resolution for 75 of these lines (Heckscher et al, 2014; Manning et al, 2012). We used this collection of sparsely-expressed Gal4 lines to express the warmth-activated TRPA1 cation channel and screen for locomotor defects in newly hatched larvae.…”
Section: Introductionmentioning
confidence: 99%
“…Such efforts introduce complementary computational challenges, e.g., the creation, integration, and comparison of static atlases of gene expression and cell-type-specific markers for the nervous system. To this end, Heckscher et al (2014) recently introduced software that addresses the general problem of building an atlas of tissues that contain cell populations in stereotyped arrangements (Figures 6E-6G). By using the transcription factor Even-skipped as a reference marker, Heckscher et al combined expression patterns from 75 Gal4 lines for the CNS of stage 16 Drosophila embryos.…”
Section: Large-scale Cell Lineage Reconstructions and Developmental Amentioning
confidence: 99%
“…Perfect prediction accuracy is indicated by a probability of 1 along the diagonal. (E) Image segmentation using the atlas building pipeline by Heckscher et al (2014). The image to the left shows a 3D rendering of a stage 16 CNS stained with antiEven-skipped (Eve).…”
Section: Large-scale Cell Lineage Reconstructions and Developmental Amentioning
confidence: 99%