Limits...
Untwisting the Caenorhabditis elegans embryo.

Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H - Elife (2015)

Bottom Line: However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis.The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo.The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

No MeSH data available.


Related in: MedlinePlus

Effects of lattice point number on untwisting results.(A) XZ and YZ views of an untwisted worm embryo using a lattice comprised of every other seam cell nucleus, a total of 12 points. This lattice fails to capture bends in the animal and does not create smooth left and right edges in the untwisted worm embryo. (B) Same as (A) but using a lattice built with all seam cell nuclei and the nose, a total of 22 points. This lattice still fails to capture some bends in the worm, and the extension of the tail. (C) Same as (A) but using a lattice built with all seam cell nuclei as well as additional points in highly bent regions in the worm embryo, plus a pair of points marking the tail, for a total of 28 points. Bends are accurately captured in the resulting untwisted volume. (D) Several additional lattice points were added to the lattice in (C), along the edges of the animal, for a total of 36 points. No noticeable improvements are apparent. Scale bar: 10 μm.DOI:http://dx.doi.org/10.7554/eLife.10070.006
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fig1s3: Effects of lattice point number on untwisting results.(A) XZ and YZ views of an untwisted worm embryo using a lattice comprised of every other seam cell nucleus, a total of 12 points. This lattice fails to capture bends in the animal and does not create smooth left and right edges in the untwisted worm embryo. (B) Same as (A) but using a lattice built with all seam cell nuclei and the nose, a total of 22 points. This lattice still fails to capture some bends in the worm, and the extension of the tail. (C) Same as (A) but using a lattice built with all seam cell nuclei as well as additional points in highly bent regions in the worm embryo, plus a pair of points marking the tail, for a total of 28 points. Bends are accurately captured in the resulting untwisted volume. (D) Several additional lattice points were added to the lattice in (C), along the edges of the animal, for a total of 36 points. No noticeable improvements are apparent. Scale bar: 10 μm.DOI:http://dx.doi.org/10.7554/eLife.10070.006

Mentions: First, seam cell nuclei are automatically detected, segmented, and paired to create candidate lattices. Seam cell segmentation and lattice-building are manually verified by a user, who can also incorporate additional information derived from pharyngeal and hypodermal markers, which are difficult to automatically segment (Figure 1D,E). Several possible lattices are generated, and the five most likely to be correct are displayed to the user for selection and editing of the correct lattice. The resulting lattice is used to generate a 3D model of the worm volume (Figure 1F, Video 1). In cases where automated lattice-building fails, lattices can be built manually by marking the positions of seam cell nuclei, nose, bends in the embryo, and tail. When manually building lattices, minimally 22 +2B lattice points are recommended (22 is the number of lattice points corresponding to seam cell nuclei, plus a pair of points to mark the nose, and B is the number of bends between seam cell nuclei in the embryo). Fewer lattice points than the number of seam cell nuclei gives unphysical, short volumes, and more than ~32 points does not noticeably improve quality in the untwisted volumes (Figure 1—figure supplement 3).Video 1.Sequential steps used in the automated lattice-building plugin.


Untwisting the Caenorhabditis elegans embryo.

Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H - Elife (2015)

Effects of lattice point number on untwisting results.(A) XZ and YZ views of an untwisted worm embryo using a lattice comprised of every other seam cell nucleus, a total of 12 points. This lattice fails to capture bends in the animal and does not create smooth left and right edges in the untwisted worm embryo. (B) Same as (A) but using a lattice built with all seam cell nuclei and the nose, a total of 22 points. This lattice still fails to capture some bends in the worm, and the extension of the tail. (C) Same as (A) but using a lattice built with all seam cell nuclei as well as additional points in highly bent regions in the worm embryo, plus a pair of points marking the tail, for a total of 28 points. Bends are accurately captured in the resulting untwisted volume. (D) Several additional lattice points were added to the lattice in (C), along the edges of the animal, for a total of 36 points. No noticeable improvements are apparent. Scale bar: 10 μm.DOI:http://dx.doi.org/10.7554/eLife.10070.006
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fig1s3: Effects of lattice point number on untwisting results.(A) XZ and YZ views of an untwisted worm embryo using a lattice comprised of every other seam cell nucleus, a total of 12 points. This lattice fails to capture bends in the animal and does not create smooth left and right edges in the untwisted worm embryo. (B) Same as (A) but using a lattice built with all seam cell nuclei and the nose, a total of 22 points. This lattice still fails to capture some bends in the worm, and the extension of the tail. (C) Same as (A) but using a lattice built with all seam cell nuclei as well as additional points in highly bent regions in the worm embryo, plus a pair of points marking the tail, for a total of 28 points. Bends are accurately captured in the resulting untwisted volume. (D) Several additional lattice points were added to the lattice in (C), along the edges of the animal, for a total of 36 points. No noticeable improvements are apparent. Scale bar: 10 μm.DOI:http://dx.doi.org/10.7554/eLife.10070.006
Mentions: First, seam cell nuclei are automatically detected, segmented, and paired to create candidate lattices. Seam cell segmentation and lattice-building are manually verified by a user, who can also incorporate additional information derived from pharyngeal and hypodermal markers, which are difficult to automatically segment (Figure 1D,E). Several possible lattices are generated, and the five most likely to be correct are displayed to the user for selection and editing of the correct lattice. The resulting lattice is used to generate a 3D model of the worm volume (Figure 1F, Video 1). In cases where automated lattice-building fails, lattices can be built manually by marking the positions of seam cell nuclei, nose, bends in the embryo, and tail. When manually building lattices, minimally 22 +2B lattice points are recommended (22 is the number of lattice points corresponding to seam cell nuclei, plus a pair of points to mark the nose, and B is the number of bends between seam cell nuclei in the embryo). Fewer lattice points than the number of seam cell nuclei gives unphysical, short volumes, and more than ~32 points does not noticeably improve quality in the untwisted volumes (Figure 1—figure supplement 3).Video 1.Sequential steps used in the automated lattice-building plugin.

Bottom Line: However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis.The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo.The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

No MeSH data available.


Related in: MedlinePlus