3DMMS

This repository is deprecated, pls refer to https://github.com/cao13jf/3DMMS_new

This program implements the 3DMMS algorithm proposed in 3DMMS: Robust 3D Membrane Morphological Segmentation of C.elegans Embryo.

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Author	Jianfeng Cao, Ming-Kin Wong, Zhongying Zhao, Hong Yan
E-mail	jfcao3-c@my.cityu.edu.hk

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Usage

• Platform dependency

This program is developed in Matlab 2017b. For computational efficiency, parallel computing is adopted in 3DMMS.

• Data preparation

All datasets are saved in .\data file. .\data\170704plc1p2\aceNuc includes the original file got from AceTree; Download raw image data from here, and put them into .\data\170704plc1p2\membrane. 170704plc1p2 corresponds to the dataset name. If you want to import other data, you can use originDataTransform.m to assemble slices into stack images.

Remember to run startup.m first to add all files into the working space.

• Parameters settting

If you want to analyze your own dataset, you might need to change parameters according to your own dataset. DTWatershed.m function includs all the parameters you need to tune. They are listed as following:

Parameter name	Meaning
data_name	membrane image dataset name
max_Time	maximal time point of the embryo stack
prescale	downsample ratio on each slice
reduceRatio	downsample ratio on the whole embryo
xy_resolution	resolution on each slice
z_resolution	distance of each slices

• Segmentation

Run DWatershed.m to implement 3DMMS segmentation on the dataset. Example results are saved in .\results\resultsWithMerge\merged_membrane, .\results_analysis\interCellFeatures and .\results_analysis\singleCellFeatures. The first one shows the segmentation results on every time points(max t=95); the second one includes the external features between neighboring cells as tree structure; the last file includes the internal features on each single cell, which is also save as tree structue.

.\example_pictures file also includes the segmentation result at t=46 for your quick reference.

• Note

1. ImageJ can be used to view *.tif files.

2. ITK-SNAP can be used to view *.nii files.

3. 3DMMS aims to segment cells in 3D, where cells closely contact to each other. Raw membrane stack images can come from C. elegans, Arabidopsis thaliana and Drosophila, but not individual cells, like cells in the blood.

Correspondence

Please contact jfcao3-c@my.cityu.edu.hk