Somitoids and segmentoids image processing. Sample code from: Miao et al., Reconstruction and deconstruction of human somitogenesis in vitro, Nature, 2022
Copyright (C) 2022 The authors
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
The code requires MATLAB (MathWorks). The code runs in MATLAB_R2022a. The code runs on a MacBook Pro (14-inch, 2021) macOS Monterey Apple M1 Pro Memory 32 GB
INSTALLATION AND USAGE - Kimographs, nematic order and spatial correlation
The user can run the code by changing MATLAB's present working directory to 'MiaoSomitogenesis2022-main'. MS Windows users have to adapt paths to MS Windows sintax.
Data files are too large to include within this Github repo and must be downloaded separately from: https://drive.google.com/file/d/15o-6nOMArxW6rLGYv5WqQHi1q7tN9ZGz/view?usp=share_link
The downloaded folder must be unzipped and tne 'data' folder must be placed in 'MiaoSomitogenesis2022-main'.
MATLAB Toolboxes required are:
- Image Processing Toolbox
- Statistics and Machine Learning Toolbox
- Signal Processing Toolbox
- Curve Fitting Toolbox
The code requires external MATLAB functions: loadtiff.m, saveastiff.m, nanconv.m, brewermap.m Those functions be downloaded from MathWorks. We attach them to the code together with their licenses.
The main image processing routine are:
- mainSegmentoidKymos.m - It generates Mesp2 and Hes7 kimographs in segmentoids and calculates their oscillation properties.
- mainNematic_segmentoid.m - It calculates the nematic order of Mesp2 signal in segmentoids. To run afte the previous.
- mainSomitoid_Mesp2Uncx.m - It calculates the spatial correlation of Mesp2, Uncx and Mesp2-Uncx signals in somitoids.
The script can run altogether or each section sequentially.
A sample dataset is provided is provided (see Installation). Expected output for each step is provided. 8Gb RAM is required. Data sample runtime: minutes.
INSTALLATION AND USAGE - SORTING FLOWS
You current Folder needs to be "MiaoSomitogenesis2022-main/sortingFlows/" while running this pipeline.
Data files are too large to include within this Github repo and must be downloaded separately from: https://drive.google.com/file/d/190IquISjvHIV3okzDnBo805sy3sXpJPW/view?usp=share_link The downloaded folder must be unzipped and the "data_tif" and "cell_struct" folders must be placed in 'MiaoSomitogenesis2022-main/sortingFlows/'.
- run experiment_*.m
- run analysis_.m except analysis__merge.m
These two steps take input from ilastik results and original movies, which are large files and not included. The outputs of these two steps are in the "cell_struct" folder from Google Drive.
The following scripts analyze different replicates of somitoid/segmentoid and are similar to each other.
- run revision2_*_tracking.m and revision2_somitoid_disp.m to produce output figures into "MiaoSomitogenesis2022-main/sortingFlows_figures/figure_revision2_segmentoid" or "MiaoSomitogenesis2022-main/sortingFlows_figures/figure_revision2_somitoid" This step takes input from "sortingFlows\cell_struct". The user will be able to run these scripts (for somitoids and segmentoids respectively)
Sample output can be downloaded from: https://drive.google.com/file/d/1ln46w0b1OtHM0Ck1z-pWpkyZt2WHaYER/view?usp=share_link
- For PIV, revision2_segmentoid_piv.m and revision2_somitoid_piv.m are used for generating preliminary PIV outputs and plots. They take input from ilastik results and original movies, which are large files that are not included.
- revision2_segmentoid_piv_find_offset.m find offsets for removing MESP2- cells, as described in Methods. Output of this step is already stored in the "cell_struct" folder.
- revision2_somitoid_piv_drawROI.m is used to manually draw ROIs for statistical tests. The generated ROIs are already stored in "cell_struct".
- revision2_segmentoid_piv_AD16oct22_1031.m generate final figures for PIV into "MiaoSomitogenesis2022-main/sortingFlows_figures/figure_revision2_segmentoid_piv", taking inputs from "cell_struct" and "data_tif".
- revision2_somitoid_piv_AD16oct22.m generate final figures for PIV into "MiaoSomitogenesis2022-main/sortingFlows_figures/figure_revision2_somitoid_piv", taking inputs from "cell_struct" and "data_tif".
Finally, source data of all figures from "sortingFlows" are generated and stored in "MiaoSomitogenesis2022-main/excel_data/"