README.Rmd

---
title: "BacTMAP"
output:
  github_document:
    fig_width: 2
    fig_height: 2
    
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
library(bactMAP)
```

## BacTMAP - Bacteria Tool for Microscopy Analysis & Plotting

<img src="man//figures//logo_bactmap_pink.png" width="200" height="200" />

This package is meant to make it easier for microbiologists to combine and analyse segmentation & fluorescence data derived from custom software like Oufti, Morphometrics, MicrobeJ or Supersegger. There are standard functions for importing several popular programs, but also options for importing CSVs or Matlab files with a specific structure. If your favorite segmentation or spot detection program is missing, don't hesitate to ask!

I use ggplot and many ggplot-extensions to make visual summaries of the segmentation & fluorescence data, show the cell genealogy, plot protein trajectories in the cell and many other things. This can give you a quick overview of your data to make a decision on further analysis and custom visualization.

In the [wiki](https://github.com/vrrenske/BactMAP/wiki) you will find a manual and some examples on how to use BactMAP as a gateway between your segmentation & fluorescence data.

**BactMAP is still in development. Not all functions listed below are fully tested & documented yet. If you have any comments, requests, please let me know!**

## Download and install package

```
#install devtools if not done yet
install.packages("devtools")

#install bactmap from my github repository
devtools::install_github("vrrenske/bactMAP")

#or install it with all dependencies
devtools::instal_github("vrrenske/bactMAP", dependencies=TRUE)

#load package
library(bactMAP)
```