index.Rmd

---
output: github_document
---

<!-- index.md is generated from index.Rmd. Please edit that file -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
# autothresholdr <img src="man/figures/logo.png" align="right" height=140/>

`autothresholdr` provides algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. It does this by porting _ImageJ_ "Auto Threshold" plugin functionality to R.

The github repo of `autothresholdr` is at https://github.com/rorynolan/autothresholdr.

## Installation

You can install the release version of `autothresholdr` from [CRAN](https://CRAN.R-project.org/package=autothresholdr) with:

```{r, eval=FALSE}
install.packages("autothresholdr")
```

You can install the development version of `autothresholdr` from [GitHub](https://github.com/rorynolan/autothresholdr/) with:

```{r, eval=FALSE}
devtools::install_github("rorynolan/autothresholdr")
```


## How to use the package

The following articles contain all you need to get going:

* [Finding Thresholds](https://rorynolan.github.io/autothresholdr/articles/finding-thresholds.html) demonstrates how to find thresholds for arbitrary non-negative integer data.
* [Thresholding Images](https://rorynolan.github.io/autothresholdr/articles/thresholding-images.html) shows how to threshold single-frame, grayscale images.
* [Thresholding Image Stacks](https://rorynolan.github.io/autothresholdr/articles/thresholding-image-stacks.html) shows a couple of approaches for thresholding multi-frame, grayscale images.