seaStarProcessingSegmentation

Main codes

codes inside: seaStarProcessingSegmentation/

mainFeaturesExtraction

Main code for extracting sea star cellular features from segmentations. Segmentations should be in .tif or .tiff format. Some paths must be changed by user --> inPath Both raw images and segmented images should be inside inPath directory. 2 Folders are needed.

DATA STRUCTURE

fullPathTo\SeaStarSegmentations
├── segmentedImages # Folder with segmented images
│ ├── SegmentedImg1.tif # Segmented image 1
│ ├── SegmentedImg2.tif # Segmented image 2
│ └── ... # etc.
├── originalImages # Folder with raw images
│ ├── OriginalImg1.tif # Raw image 1
│ ├── OriginalImg2.tif # Raw image 2
│ └── ... # etc
└──

mainFeaturesExtractionBulk

Same as mainSegmentation but for processing several folders. Main code for extracting sea star cellular features from segmentations. Segmentations should be in .tif or .tiff format. Some paths must be changed by user --> inPath Both raw images and segmented images should be inside each one of the inPath folders

DATA STRUCTURE

fullPathTo\SeaStarSegmentations
├── segmentedImages # Folder with segmented images
│ ├── SegmentedImg1.tif # Segmented image 1
│ ├── SegmentedImg2.tif # Segmented image 2
│ └── ... # etc.
├── originalImages # Folder with raw images
│ ├── OriginalImg1.tif # Raw image 1
│ ├── OriginalImg2.tif # Raw image 2
│ └── ... # etc
└──

mainGetVoronoiModels

Main code for whole voronoi packing processing for comparing voronoi models against real data. Uses getVoronoiModels function

User must change some paths.

DATA STRUCTURE

fullPathTo\SeaStarSegmentations
├── segmentedImages # Folder with segmented images
│ ├── SegmentedImg1.tif # Segmented image 1
│ ├── SegmentedImg2.tif # Segmented image 2
│ └── ... # etc.
├── originalImages # Folder with raw images
│ ├── OriginalImg1.tif # Raw image 1
│ ├── OriginalImg2.tif # Raw image 2
│ └── ... # etc
└──

mainCurvatureEmbryoSurface

Main code for curvature analysis of the SeaStar embryo. Coordinates of outter layer cell centroids and inner layer cell centroids are needed. Inner layer and outer layer can be extracted using getInnerOuterLateralFromEmbryos An excell file with estimated info of all 3 principal axes of the embryo are needed as well as estimated mean cell height. This was done manually using FIJI.

inPath directory should have a folder for each movie. Inside those folders, a folder for each one of the 3 stages. Then, inside those folders, all timepoints (.tif) and a .mat file with relevant information of the original images. This can be extracted using mainSegmentation.m

DATA STRUCTURE

D:\Path\to\curvatureAnalysis\data
├── excellFile.xls
├── movie1 # Folder with movie 1 data
│ ├── originalImageName.mat # Relevant data of raw images (obtained using FIJI)

│ │ ├─stage128
│ │ │ ├── timepoint1.tif # Segmented image stage 128 timepoint 1
│ │ │ ├── timepoint2.tif # Segmented image stage 128 timepoint 2
│ │ │ └── ... # etc.
│ │ ├─stage256
│ │ │ ├── timepoint1.tif # Segmented image stage 256 timepoint 1
│ │ │ ├── timepoint2.tif # Segmented image stage 256 timepoint 2
│ │ │ └── ... # etc.
│ │ ├─stage512
│ │ │ ├── timepoint1.tif # Segmented image stage 512 timepoint 1
│ │ │ ├── timepoint2.tif # Segmented image stage 512 timepoint 2
│ │ │ └── ... # etc.
├── movie2 # Folder with movie 2 data
│ └── ... # etc.
└── ...

.mat table structure

ID_Tissue	Major_Axis	Major_Axis	Minor_Axis	Avg_CellHeight
tissue_1	123.45	123.45	123.45	123.45
...	...	...	...	...

Note: There is two major axis columns since we assume oblate embryoids.

Voronoi

codes inside: seaStarProcessingSegmentation/Voronoi/

GetVoronoiModels

Function to make voronoi tesselations from centroids of image segmentations. It is used to compare voronoi models with real data. This function is called from seaStarProcessingSegmentation/maiGetVoronoiModels

INPUTS:

originalImage: raw image
labelledImage: segmented image

OUTPUTS:

voronoiSeaStar: voronoi tesselation

featuresExtraction

codes inside: seaStarProcessingSegmentation/featuresExtraction

Codes for feature extraction called by the main codes: tissue and cell morphological features, scutoids data, and code for aggregate the data into a table.

Documentation can be found inside the .m files.

preprocessing

codes inside: seaStarProcessingSegmentation/preprocessing

Codes for sea star embryos preprocessing. Needed for a correct cell segmentation.

Documentation can be found inside the .m files.

utils

codes inside: seaStarProcessingSegmentation/utils General useful codes.

Documentation can be found inside the .m files.

cartoStar

codes inside: seaStarProcessingSegmentation/cartoStar

Codes for cartographic representation of sea star features.

Main code is "cartoStar.m". The output of this code consists of two images, one in BMP format and another in PNG format. These images represent: sea star top (random colors), sea star bottom (random colors), sea star bottom (colored based on volume), sea star bottom (colored based on solidity), sea star bottom (colored if scutoid).