update readme

Author: ahillsley

README.md

@@ -1,15 +1,54 @@
 blinx
 =====
+A Bayesian method to Count the Number of Molecules within a Diffraction Limited Spot
+--
 
-A tool to estimate the number of blinking fluorescent molecules in a spatially un-resolvable region.
+- **[Introduction](#introduction)**
+- **[Installation](#installation)**
+- **[Examples](#examples)**
+- **[Citation](#citation)**
 
 
-Check out the [documentation](https://funkelab.github.io/blinx/)
+# Introduction
+This repository contains code to estimate the number of fluorescent emitters
+when only their combined intensity can be measured.
 
+`blinx` directly models the photo-physics of the system as well as temporal 
+fluctuations in intensity to produce a probabilistic estimate of the molecular count.
 
-`blinx` is designed to work with any type of stochastically blinking emitters, but was specifically built with the analysis of 
-[DNA-PAINT](https://www.nature.com/articles/nprot.2017.024) experiments in mind.
+![iamge](imgs/overview.pdf)
 
+Detailed documentation can be found: [here](https://funkelab.github.io/blinx/)
 
-At the base level, `blinx` works on a piece of data called the *intensity trace*, which is an ordered sequence of intensity measurements over time. 
+# Installation
+For a basic CPU installation:
+```bash
+conda create -n blinx python
+conda activate blinx
+git clone https://github.com/funkelab/blinx.git
+cd blinx
+pip install .
+```
 
+For a GPU installation specific versions of jax and jaxlib must be pinned: 
+```bash
+conda create -n blinx python cudatoolkit=11.4 cudatoolkit-dev=11.4 cudnn=8.2 -c conda-forge
+conda activate blinx
+git clone https://github.com/funkelab/blinx.git
+cd blinx
+pip install .
+pip install 'jax==0.4.1' 'jaxlib==0.4.1+cuda11.cudnn82' -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+
+```
+# Examples
+`blinx` contains two primary modules. An estimate module to determine the posterior over molecular count, 
+and a forward model to generate simulated traces from a given set of parameters.
+
+### Fitting:
+
+`blinx.estimate`
+
+
+### Forward Model:
+
+`blinx.trace_model.generate_trace`