Cell shape analysis

Cell shape analysis
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This package contains custom-written code associated with the paper "Direct observation of a crescent-shape chromosome in Bacillus subtilis" By Tišma et al. 2023

See README's in subdirectories for specific content description 

Notes:
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## general
* code for extended cell analysis as used in the Cees Dekker Lab, 2017-onwards

## associated publications
1. [current submission] 'Direct observation of a crescent-shape chromosome in Bacillus subtilis'
Authors Miloš Tišma, Florian Patrick Bock, Jacob Kerssemakers, Aleksandre Japaridze, Stephan Gruber, Cees Dekker, submitted (2023).

2. MukBEF-dependent chromosomal organization in widened Escherichia coli
Authors Aleksandre Japaridze, Raman van Wee, Christos Gogou, Jacob WJ Kerssemakers, Cees Dekker; (2022)
3. Direct observation of independently moving replisomes in Escherichia coli
Authors Aleksandre Japaridze, Christos Gogou, Jacob WJ Kerssemakers, Huyen My Nguyen, Cees Dekker, Nat.Com (2020)
4. Direct imaging of the circular chromosome in a live bacterium
Authors Fabai Wu, Aleksandre Japaridze, Xuan Zheng, Jakub Wiktor, Jacob WJ Kerssemakers, Cees Dekker, Nat.Com (2019)

## package description
This package collects code to analyze multi-channel microscope images of cells. Patterns of interest may be extended, such as a fully labeled chromosome, or compact, as one or multiple labeled spots. The code is used to select and screen individual cells and to quantify locations of above labels. 

## package contents
* custom-written source code [Matlab] 
* test data to demonstrate the software code

## system requirements and used software
* Windows 10, 64bits 
* Matlab Version 2021 [custom source code]
* Oufti Version .... 
* Fiji(ImageJ) Version 1.52a
* Dip_image analysis software Version 2.9

## installation guide
* please follow the installation instructions provided by above package distributors
* installation of all platforms should take less than a day on a standard PC

## demo and instructions for use
* the code is divided in three main subsections (that are to be used in this order) and one extra:
    * 'crop': works on microsocopic data, outputs data organized per cells
    * 'donut': in-depth analysis on chromosome patterns and other labels ('spots')
    * 'repli': follow-up analysis on spots
    * 'topical subjects': shorter code platforms for various analyses
* see 'README.md' in each subdirectory for a detailed step-by-step descriptions, in order of appearance or importance in the analysis pipeline
* see 'README_code_annotations.md' in each subdirectory for a full collection of all custom function descriptions
* demo data for two cells is provided to illustrate workings and settings. Running this demo data typically only takes a few minutes
* for new data, follow the setup as described via the demo data 

## contributions
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* F. Wu and X. Zheng originally wrote and assembled the original code package
* J.Kerssemakers organized, re-edited and expanded the 'crop' code package
* J.Kerssemakers wrote the 'donut' and 'repli' code packages
* A. Japaridze, Raman van Wee, Christos Gogou and M.Tisma contributed to analysis design
* J.Kerssemakers and M.Tisma contributed to 'topical subjects'

## disclaimer
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This code was custom written and shared to illustrate used algorithms, analysis pathways etc. in relation to published results. The code was regularly used and tested. However, small bugs, not relevant for the data analysis as present in publications may still be around. Interested users are expected to have a sufficient knowledge of Matlab code to understand and adapt the code to their own wishes.

细胞形态分析（Cell shape analysis）
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本软件包包含与Tišma等人2023年发表的论文《枯草芽孢杆菌（Bacillus subtilis）中新月形染色体的直接观测》（Direct observation of a crescent-shape chromosome in Bacillus subtilis）相关的定制编写代码。

有关具体内容说明，请参阅各子目录中的README文件

注释：
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## 通用说明
* 本代码为Cees Dekker实验室自2017年起使用的拓展细胞分析代码

## 关联发表成果
1. 【当前投稿论文】《枯草芽孢杆菌（Bacillus subtilis）中新月形染色体的直接观测》（Direct observation of a crescent-shape chromosome in Bacillus subtilis）
作者：Miloš Tišma、Florian Patrick Bock、Jacob Kerssemakers、Aleksandre Japaridze、Stephan Gruber、Cees Dekker，2023年已投稿

2. 《增宽大肠杆菌（Escherichia coli）中依赖MukBEF的染色体组织》（MukBEF-dependent chromosomal organization in widened Escherichia coli）
作者：Aleksandre Japaridze、Raman van Wee、Christos Gogou、Jacob WJ Kerssemakers、Cees Dekker，2022年

3. 《大肠杆菌（Escherichia coli）中独立移动的复制体（replisomes）的直接观测》（Direct observation of independently moving replisomes in Escherichia coli）
作者：Aleksandre Japaridze、Christos Gogou、Jacob WJ Kerssemakers、Huyen My Nguyen、Cees Dekker，发表于Nat.Com，2020年

4. 《活细菌中环状染色体的直接成像》（Direct imaging of the circular chromosome in a live bacterium）
作者：Fabai Wu、Aleksandre Japaridze、Xuan Zheng、Jakub Wiktor、Jacob WJ Kerssemakers、Cees Dekker，发表于Nat.Com，2019年

## 软件包说明
本软件包集成了用于分析细胞多通道显微镜图像的代码。所关注的图像模式既可以是延展型（如完全标记的染色体），也可以是紧致型（如单个或多个标记位点）。本代码可用于筛选单个细胞，并对上述标记物的位置进行定量分析。

## 软件包内容
* 定制编写的Matlab源代码
* 用于演示软件功能的测试数据

## 系统与软件依赖
* Windows 10 64位系统
* Matlab 2021版本（适配本定制源代码）
* Oufti 版本（原文未注明具体版本号）
* Fiji(ImageJ) 1.52a版本
* Dip_image 分析软件 2.9版本

## 安装指南
* 请遵循上述各软件分发方提供的安装说明进行安装
* 在标准个人电脑上完成全平台安装耗时通常不超过一天

## 演示与使用说明
* 本代码分为三个主模块（需按顺序使用）及一个附加模块：
* 'crop（图像裁剪）'：处理显微镜图像数据，输出按细胞整理的数据集
* 'donut（环形分析）'：对染色体模式及其他标记位点进行深度分析
* 'repli（复制体分析）'：针对标记位点的后续分析
* 'topical subjects（专题模块）'：用于各类分析的轻量化代码平台
* 请参阅各子目录中的README.md文件，按照分析流程的顺序或重要性获取详细的分步操作说明
* 请参阅各子目录中的README_code_annotations.md文件，获取所有定制函数的完整说明
* 本软件包提供了两个细胞的演示数据，用于展示代码功能与参数设置。运行该演示数据通常仅需数分钟
* 针对新的数据集，请参照演示数据中描述的流程进行参数配置

## 贡献者说明
* F. Wu与X. Zheng最初编写并整合了本原始代码包
* J.Kerssemakers对crop模块代码包进行了整理、重编辑与拓展
* J.Kerssemakers编写了donut与repli模块代码包
* A. Japaridze、Raman van Wee、Christos Gogou与M.Tisma参与了分析框架的设计
* J.Kerssemakers与M.Tisma参与了专题模块的开发

## 免责声明
本代码为定制编写，旨在展示与已发表研究成果相关的算法、分析流程等内容。本代码曾被常规使用与测试，但仍可能存在与论文中数据分析无关的细微漏洞。有意向使用的用户需具备足够的Matlab代码知识，以便理解并根据自身需求对代码进行调整。