ASTEC

Posted on 7 May 2020

DESCRIPTION

ASTEC (Automated Segmentation and Tracking of Embryonic Cells) is a software library designed to segment and track in time all cells of a developing embryo, whose cell membranes are fluorescently labelled and which is imaged live every 2 minutes by multiview light-sheet microscopy.

The library includes several modules, which can be used independently or in combination and in particular: 

1) Fusion and cropping of the different stacks generated during multiview imaging. This module produces for each timepoint an isotropic resolution image that selects the best region of each image stack taken in multiview imaging mode.

2) One pass segmentation and tracking of individual cells. This module (and its submodules) segments each time point and propagates the segmentation to the next time point, thereby allowing the reconstruction of full cell lineage trees.

3) Post-correction. This module identifies and corrects residual oversegmentation events.

The Astec project is collaborative effort by the transcriptional control of chordate morphogenesis team at CRBM Montpellier, the Mosaic team at RDP Lyon, and the Morpheme team at Sophia Antipolis.

ASTEC was published in Science: Guignard L, Fiúza UM, Leggio B, Laussu J, Faure E, Michelin G, Biasuz K, Hufnagel L, Malandain G, Godin C, Lemaire P. Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis. Science. 2020 Jul 10; 369(6500):eaar5663. An earlier description was also posted as a bioRxiv preprint.

SOFTWARE

The software, standard parameters files and tutorials can be found in the Github repository: https://github.com/astec-segmentation

astec-2019-published is the repository dedicated to this paper with a fixed and autonomous (full version, python and C codes) ASTEC software package. This includes all the codes and libraries necessary to install the software with examples as standard parameters files and a tutorial to test it. A complete documentation is also provided to guide the users.
 
Astec is the repository for the ongoing development, enhancement and storage. Only the python codes are included in this repository. The standard parameter files or tutorial provided in the astec-2019-published repository may have to be adapted to more recent versions of the code.
 
Standard parameters. We provide a standard example parameter file that can be initially used to setup each ASTEC step on either the test set we provide (see below) or to initiate a project on personal data.
 
Tutorial and test dataset. We provide a tutorial to test each step of ASTEC, a set of 20 timepoints from ASTEC-Pm1 with a downsized resolution to 1μm3. The ASTEC pipeline on this dataset can be run on a standard workstation (4 threads; < 1 mn for the fusion and segmentation of a timepoint).
 
A Jupyter notebook providing examples on how to use the outputs of ASTEC can be found in the Github repository: https://github.com/leoguignard/ASTEC-examples.

DATASETS
 
The imaging, segmentation and geometric informations for two wild-type Phallusia mammillata embryos imaged with a MuViSPIM and processed with ASTEC can be downloaded from our Figshare Phallusia mammillata project. For each embryo several archives can be downloaded:
  • Raw images: The four views for some time points of the movie ASTEC-Pm1 are shared to test the fusion algorithms or evaluate the quality of the acquisitions obtained with the MuViSPIM light-sheet microscope (raw.tar.gz archive). The format of the image files, .hdf5, can be easily read with an ImageJ/FIJI plug-in.
  • Fused images: complete sequence of fused images are shared for ASTEC-Pm1 to -Pm10 (fuse.tar.gz archive file). A tool is provided in the astec-2019-published Github repository to convert .inr format files into the more common .mha files
  • Segmented images: complete sequence of segmented images (voxelic representation) are provided for the entire ASTEC dataset (post.tar.gz archive file).
  • Meshed segmented images: a meshed version of the segmented images (.obj format) produced using the VTK library and MeshLab is provided for all embryos (mesh.tar.gz archive) and can be explored into the interactive Morphonet web tool.
  • Geometric properties: Properties (cell lineage, cell volume, cell neighbors, areas of cell contact…) measured after spatial registration of the movies are shared in both .pkl and .xml format for all embryos (properties.tar.gz archive file).

Data S1. Astec-Pm1. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 8-17 (64-cell to initial tailbud 1). To download data: https://figshare.com/articles/dataset/Astec-Pm1_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_8-17_/8223890. To explore data in Morphonet: http://morphonet.org/vRUmNqjT

Data S2. Astec-Pm2. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 8-15 (64-cell to mid neurula). To download data: https://figshare.com/articles/dataset/Astec-Pm2_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_8-15_/8235443. To explore data in Morphonet: http://morphonet.org/FNOt1fpq

Data S3. Astec-Pm3. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 7-13 (44-cell to late gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm3_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_7-13_/8235449. To explore data in Morphonet: http://morphonet.org/GmcStH8u

Data S4. Astec-Pm4. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 6-12 (32-cell to mid gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm4_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-12_/8235455. To explore data in Morphonet: http://morphonet.org/f9lfraWa

Data S5. Astec-Pm5. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 7-13 (44-cell to late gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm5_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_7-13_/8235458. To explore data in Morphonet: http://morphonet.org/SbEIO8tC

Data S6. Astec-Pm6. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 7-13 (44-cell to late gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm6_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_7-13_/8235470. To explore data in Morphonet: http://morphonet.org/8D0hxclb

Data S7. Astec-Pm7. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 7-12 (44-cell to mid gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm7_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_7-12_/8235473. To explore data in Morphonet: http://morphonet.org/oatmlvo9

Data S8. Astec-Pm8. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 8-14 (64-cell to early neurula). To download data: https://figshare.com/articles/dataset/Astec-Pm8_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_8-14_/8235479. To explore data in Morphonet: http://morphonet.org/TO1r1t8T

Data S9. Astec-Pm9. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 8-12 (64-cell to mid gastrula). To download data: https://figshare.com/articles/dataset/Astec-Pm9_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_8-12_/8235482. To explore data in Morphonet: http://morphonet.org/WyBygTPt

Data S10. Astec-Pm10. Wild type Phallusia mammillata embryo, live SPIM imaging, stages 7-17 (44-cell to initial tailbud 2). To download data: https://figshare.com/articles/dataset/Astec-Pm10_Wild_type_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_7-17_/8235485. To explore data in Morphonet: http://morphonet.org/febECUjB