Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

Abstract

During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic.

The role ofatoh1genes in the development of the lower rhombic lip during zebrafish hindbrain morphogenesis

“…For the quantification of the delamination time of atoh1a:cells in atoh1a WT and atoh1a fh282 embryos in the Tg[atoh1a:GFP] background, we kept track of the time of division of a given cell (t0) and the time of delamination of the resulting cells (tf) and calculated the difference between tf and t0 ( Figure 5K). Cell tracking was performed using the MaMuT software (Fiji plug-in) [49].…”

BioCell2XML: A novel tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji)

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Computer-assisted 4D manual cell tracking has been a valuable method for understanding spatial-temporal dynamics of embryogenesis (e.g., Stach & Anselmi, 2015;Vellutini et al, 2017;Wolff et al, 2018) since the method was introduced in the late 1990s. Since two decades SIMI® BioCell (Schnabel et al, 1997), a software which initially was developed for analyzing data coming from the, at that time new technique of 4D microscopy, is in use.Many laboratories around the world use SIMI BioCell for the manual tracing of cells in embryonic development of various species to reconstruct cell genealogies with high precision.However, the software has several disadvantages: Limits in handling very large data sets, the virtually no maintenance over the last ten years (bound to older Windows versions), the difficulty to access the created cell lineage data for analyses outside SIMI BioCell, and the high cost of the program.

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“…Since two decades SIMI® BioCell (Schnabel et al, 1997), a software which initially was developed for analyzing data coming from the, at that time new technique of 4D microscopy, is in use.Many laboratories around the world use SIMI BioCell for the manual tracing of cells in embryonic development of various species to reconstruct cell genealogies with high precision.However, the software has several disadvantages: Limits in handling very large data sets, the virtually no maintenance over the last ten years (bound to older Windows versions), the difficulty to access the created cell lineage data for analyses outside SIMI BioCell, and the high cost of the program. Recently, bioinformatics, in close collaboration with biologists, developed new lineaging tools that are freely available through the open source image processing platform Fiji.Here we introduce a software tool that allows conversion of SIMI BioCell lineage data to a format that is compatible with the Fiji plugin MaMuT (Wolff et al, 2018). Hereby we intend to maintain the usability of SIMI BioCell created cell lineage data for the future and, for investigators who wish to do so, facilitate the transition from this software to a more convenient program.…”

“…Computer-assisted 4D manual cell tracking has been a valuable method for understanding spatial-temporal dynamics of embryogenesis (e.g., Stach & Anselmi, 2015;Vellutini et al, 2017;Wolff et al, 2018) since the method was introduced in the late 1990s. Since two decades SIMI® BioCell (Schnabel et al, 1997), a software which initially was developed for analyzing data coming from the, at that time new technique of 4D microscopy, is in use.…”

“…Here we introduce a software tool that allows conversion of SIMI BioCell lineage data to a format that is compatible with the Fiji plugin MaMuT (Wolff et al, 2018). Hereby we intend to maintain the usability of SIMI BioCell created cell lineage data for the future and, for investigators who wish to do so, facilitate the transition from this software to a more convenient program.…”