DOI: 10.5061/dryad.xpnvx0kvd
title: Data from: Cilia-driven epithelial folding and unfolding in an early-diverging animal

description: Multicellular organisms utilize epithelial folding to achieve remarkable
 three-dimensional forms. During embryonic development, stereotypical
 epithelial folds emerge from underlying active cellular and molecular
 processes including cell shape change and differential cell growth.
 However, the origin of epithelial folding in early animals and how folding
 may be harnessed in synthetic systems remain open questions. Here we
 discover a novel modality of behavior-induced epithelial folding and
 unfolding arising from cilia-substrate adhesion and ciliary walking in the
 basal animal Trichoplax adhaerens (phylum Placozoa). We show that T.
 adhaerens is capable of exhibiting dynamic non-stereotyped folding states,
 providing a novel 3D perspective to an organism previously only
 characterized in its 2D state. We correlate these folding states to local
 substrate geometry, revealing that the animal conforms to available
 substrate surface area, promoting the maintenance of a folded state. Using
 4D fluorescence light sheet microscopy, we characterize fold geometry,
 curvature evolution during unfolding, and the non-stereotypy of unfolding
 behavior. Through repeated unfolding trials, we reveal the robustness and
 timescales associated with unfolding behavior and employ scaling analysis
 and toy model simulations to establish how collective ciliary activity can
 robustly drive unfolding. In this way, despite lacking any
 folding-unfolding "pathway," transitions between folding and
 unfolding states emerge as a function of the animal’s environment and
 motility. Our work reveals a remarkable behavior exhibited by a brainless,
 nerveless animal, and demonstrates the capacity for 3D-2D transitions in
 folding epithelial sheets using ciliary activity.
description: # Data from: Cilia-driven epithelial folding and unfolding in an
 early-diverging animal Dataset DOI:
 [10.5061/dryad.xpnvx0kvd](https://doi.org/10.5061/dryad.xpnvx0kvd) ##
 Description of the data and file structure The following datasets were
 collected in support of the study of cilia-driven folding and unfolding
 behavior exhibited by the early-diverging animal *Trichoplax adhaerens*.
 The headings below correspond to zip files included in this dataset. 
 Animal numbering (e.g., "animal1") is not preserved throughout
 the dataset, and only serves to organize data within a given section. ####
 1. animal folding on glass capillaries This section contains data from
 experiments testing *T. adhaerens'* folding state as a function of
 substrate geometry. Animals were allowed to attach to the surface of a
 glass capillary of either 1mm or 0.17mm outer diameter, suspended in a
 dish of artificial sea water. * The directory structure is `[capillary
 diameter] / [unfolding trial]` * `animal_area_on_capillary.py`:  Python
 script to extract and plot the maximum diameter of the animal contour as
 it is in contact with the capillary.   #### 2. animal folding without
 substrate This section contains data from experiments testing *T.
 adhaerens'* folding state in the absence of a rigid substrate.
 Animals were imaged in artificial sea water suspended in an annular
 imaging chamber. * The directory structure is `[animal] / [image dir]`,
 where the image_dir contains a maximum of 1000 images.  *
 `tplax_area_no_substrate.py`:  Python script to extract and plot the
 maximum diameter of the animal contour as it is suspended in the vertical
 tracking microscope. #### 3. animal unfolding trials - size This section
 contains data from experiments testing *T. adhaerens'* unfolding
 trajectory as a function of animal size. * The directory structure is
 `[animal] / [unfolding trial number]`.  *
 `animal_size_unfolding_times.csv`: Table of unfolding times in provided
 directories. * `animal_size_unfolding_time_regression.py`:  Python script
 to compute unfolding time statistics as a function of animal size, and
 plot animal size vs. unfolding time statistic with linear regression of
 the same. `animal_size_unfolding_times.csv` provides the input data to
 this script. * `animal_size_unfolding_time_violinplot.py`:  Python script
 to visualize the distribution of unfolding times sorted by animal
 identity. `animal_size_unfolding_times.csv` provides the input data to
 this script. #### 4. cellular perspective in folds - confocal This section
 contains data from confocal imaging of fixed *T. adhaerens'* in a
 folded state. * `fixed fold hoechst and membrane stain.czi`: raw 2-channel
 imaging file from confocal microscopy session. Channels show membrane
 stain (red) and nuclear stain (green). * `fixed fold hoechst and membrane
 stain.ims`: imaris file with oblique slicer to visualize the fold profile.
 Same data as in `fixed fold hoechst and membrane stain.czi.` #### 5.
 animal folding snapshots - light sheet This section contains data from
 light sheet imaging of live and fixed *T. adhaerens'* in a folded
 state. * The directory structure is `[animal] / [data files] / [raw data]`
 * Snapshot 6 is of a fixed animal while all other snapshots are of live
 animals. #### 6. silicone rubber sheet unfolding This section contains
 data from unfolding time lapses of silicone rubber sheets on glass
 surfaces coated with silicone oil. * This directory contains an image
 directory (labeled 1-10) and a corresponding results file (labeled
 `[n]_Results.csv`). The results files contain pixel area values for
 imaging data. - `rubber_sheet_unfolding.csv`: Python script to visualize
 the contact area over time for rubber sheet unfolding time lapses. Plots
 data in results files in an overlay plot. #### 7. animal unfolding trials
 - light sheet This section contains data from unfolding time lapses of
 fluorescently labeled live *T. adhaerens* captured via light sheet
 microscopy. * This directory structure is `[animal id] / [time lapse
 part]` #### 8. animal 3D curvature maps This section contains local
 curvature maps of light sheet data, obtained using MeshLab.  #### 9.
 animal unfolding trials - LiCl and CFSW This section contains unfolding
 trials for animals treated in a sequence of artificial sea water, either
 calcium-free sea water (CFSW) or 200 mM lithium chloride, and artificial
 sea water again.  * `./CFSWtrials`: contains calcium-free sea water
 unfolding trials.  `./CFSWtrials/Raw images` contains the image sequence
 for each unfolding trial. `Ignore_[filename]` files contain any frames to
 ignore due to segmentation issues. `Results_[filename]` files contain
 contact area data in pixels.  * `./LiCl trials`: contains 200 mM lithium
 chloride in sea water unfolding trials.  `./LiCl trials/Raw images`
 contains the image sequence for each unfolding trial. `Ignore_[filename]`
 files contain any frames to ignore due to segmentation issues.
 `Results_[filename]` files contain contact area data in pixels.  *
 `licl_cfsw_unfolding.py`: Python script to plot contact area vs. time for
 all unfolding trials in this section, organized by treatment type and
 whether the trial is pre-treatment, treatment, or post-treatment. #### 10.
 animal unfolding trials -unfolding time distribution This section contains
 unfolding time lapses used to obtain unfolding times across a distribution
 of animals. * `./additional unfolding timelapses/`: contains 45 additional
 unfolding time lapses which, together with the data included in (3) above,
 are used to obtain an unfolding time distribution. *
 `animal_size_unfolding_times_all.csv`: Unfolding time data from 163
 unfolding time lapses, annotated by animal identity, size, and trial. *
 `animal unfolding times distribution.py`: Python script to plot the
 distribution of unfolding times in `animal_size_unfolding_times_all.csv`.