Figure 1. Regions of interest are followed in time by browsing the cell lineages.

(A) Largest population of cells (purple) that remains visible throughout the entire time-lapse. Two cell rows in contact to margin cells were discarded as margin cells are usually not well segmented. (B) Largest blade cell population (green) that remains visible throughout the entire time-lapse. The blade region of interest (yellow line) was defined on the last frame of the time-lapse using a custom Fiji macro (https://github.com/mpicbg-scicomp/tissue_miner/blob/master/fiji_macros/). The underlying cell population was then subset using our lineage browser algorithm. (C) One can define veins and inter-vein regions of interest and apply the same algorithm as in (B). (D–D') Regularly spaced regions of interest automatically selected and followed over time to visualize tissue deformation. (E–E') Here, we make use of the lineage browser routine to trace back the vein positions at 15 hAPF, as they aren't visible yet at 15 hAPF. Scale bar 50 microns.

DOI: http://dx.doi.org/10.7554/eLife.14334.004

Figure 1—figure supplement 1. Flow chart of TissueMiner.

Solid lines depict the three main steps to analyze epithelial morphogenesis within TissueMiner. Dashed lines indicate additional inputs to the automated workflow: red boxes represent required inputs and black boxes indicate optional inputs. Arabic numbers indicate the order in which the tools are described in the main text. Cumulative time of the movie must be listed in a text file called cumultimesec.txt and located along with the movie images. The snakemake automated workflow is described in Figure 7.

DOI: http://dx.doi.org/10.7554/eLife.14334.005