DOI: 10.5061/dryad.wstqjq30g
title: Microscopy images from: A cadherin-integrin-ECM code for presomitic mesoderm fluidity

description: Animal tissues exist within a continuum of fluid to solid states, and
 transitions between states are important for embryonic development, wound
 healing and cancer metastasis. Fluid to solid transitions are governed by
 the ratio of adhesive energy to kinetic energy. Here, we find that
 presomitic mesoderm solidification is driven by an intrinsic decline in
 cell speed along with an increase in adhesion mediated by Cadherin 2 in
 parallel with Fibronectin and its receptor Integrin α5. A computational
 model of cell-cell adhesion in the central tissue mesenchyme and cell-ECM
 adhesion on the tissue surface explains the observed phenotypes. Further,
 we identify negative feedback within the ECM as Fibronectin supports the
 formation of a separate layer of Fibrillin 2b matrix that inhibits
 solidification. These data reveal a tissue fluidity code in which
 solidification is promoted by cadherins in parallel with Integrin α5 and
 Fibronectin, whereas negative feedback through Fibrillin 2b promotes
 fluidization.
description: # Microscopy images from: A cadherin-integrin-ECM code for presomitic
 mesoderm fluidity Dataset DOI:
 [10.5061/dryad.wstqjq30g](https://doi.org/10.5061/dryad.wstqjq30g) ##
 Description of the data and file structure This dataset contains
 microscopy images of the zebrafish PSM obtained for the purpose of
 calculating cell shape and packing fraction (Figure 2), cell velocity
 (Figure 3), and ECM structure (Figure 5) in A cadherin-integrin–ECM code
 for presomitic mesoderm fluidity.  ### Files and variables #### File:
 cellposemodels.zip **Description:** Custom trained Cellpose 2.0 models for
 segmenting cells in coronal and transverse orientations using membrane-RFP
 and secreted-GFP. See Figure 2C and S4. Two models: one for XY and one for
 XZ orientation for use with cellpose 2.0 XY model: itgcdh_xy_gray Trained
 on images of MZ-itga5-; cdh2- expressing memRFP, secreted GFP,
 Segmentation done in grayscale ie channels=[0, 0] Presumably
 cellposes's grayscale conversion is 1/2 red intensity + 1/2 green
 intensity. XZ model: XZ_quarterweight Trained on a  variety of wt, cdh2-
 and MZ-itga5-, cdh2- embryos; memRFP, secreted GFP orthogonal reslice
 images Segmentation done on custom grayscale image calculated as red
 intensity + 1/4 green intensity, saved as 16 bit image. Import model with
 command: model = models.CellposeModel(pretrained_model=file path to model,
 model_type=model name) Run segmentation with: model.eval(image, channels,
 diameter) #### File: secretedGFP_zstack.zip **Description:** Confocal
 z-stacks of embryos expressing membrane RFP and secreted GFP. File name
 pattern is genotype \_ embryoID \_ PSM ID.czi See Figure 2A. #### File:
 timelapses.zip **Description:** Confocal z-stack, time-lapse of embryos
 expressing histone 2A-GFP. Frame rate is 3 minutes. File name pattern is
 date \_ genotype \_id.czi See Figure 3. #### File: ECMfibers.zip
 **Description:** Max projection of Airyscan images of dorsal PSM surface
 of knock-in embryos with fb2nb-mScarlet1 and/or fn1a-mNG. Each sub-folder
 contains embryos with a specific genotype (wild-type, fbn2b-, fn1a-;
 fn1b-). Channel order in wild-type is mScarlet then mNG. File name pattern
 is generally date-fluorescent alleles-genotype-10som-embryo id-PSM id.
 File format is multipage tiff. Pixel size is 0.1 micron. See Figure 5. ##
 Code/software Images can be viewed with ImageJ. Cell segmentation is
 performed with Cellpose v2.0.