Updated readme

README.md

 # SlideR :hamburger: : Slide Registration tools
+
+Collection of registration tools for microscopy.
+
+Built upon the Tensor Image Registration Library: https://git.fmrib.ox.ac.uk/ihuszar/tirl
+
+## Dependencies
+
+You will need to download and install miniconda to manage the python environment:
+https://docs.conda.io/en/latest/miniconda.html
+
+## Installation
+First clone TIRL:
+```shell
+git clone https://git.fmrib.ox.ac.uk/ihuszar/tirl.git
+```
+
+Create a virtual environment for SlideR:
+```shell
+conda env create -n slider -f tirl/tirlenv.yml
+conda activate slider
+```
+
+Install TIRL:
+```shell
+cd tirl
+python setup.py install
+cd ..
+```
+
+Install SlideR:
+```shell
+git clone https://git.fmrib.ox.ac.uk/seanf/slider.git
+pip install -e slider
+```
+
+## Usage
+
+### Register 2D-slide to 2D-slide
+
+You can register a 2D-slide to a 2D-slide using the `SLIDE` subcommand of the `slider_app.py` app.
+
+```shell
+>> slider_app.py SLIDE -h
+
+usage: slider_app.py SLIDE [-h] [--out <dir>] [--config <config.json>]
+                           <moving> <moving-resolution> <fixed> <fixed-resolution>
+
+Register 2D slide to 2D slide
+
+positional arguments:
+  <moving>                Moving slide image
+  <moving-resolution>     Moving image resolution (mm)
+  <fixed>                 Fixed slide image
+  <fixed-resolution>      Fixed image resolution (mm)
+
+optional arguments:
+  -h, --help              show this help message and exit
+  --out <dir>             Output directory
+  --config <config.json>  configuration file
+```
+
+For example:
+
+```shell
+slider_app.py SLIDE \
+    mr247MBP_c24_s20a.jp2 0.0004 \
+    mr247NeuN_c01_s19n.jp2 0.0004 \
+    --out=mr247_mbp_to_neun.reg
+```
+
+### Apply transform to image
+
+Once registered, you can apply the transform to the native image using the `APPLYXFM` subcommand of the `slider_app.py` app.
+
+```shell
+>> slider_app.py APPLYXFM -h
+usage: slider_app.py APPLYXFM [-h] [--inverse]
+                              <moving> <moving-resolution> <fixed> <fixed-resolution> <reg-moving>
+                              <reg-fixed> <resampled-img>
+
+Apply transform to image.
+
+positional arguments:
+  <moving>             Moving slide image
+  <moving-resolution>  Moving image resolution (mm)
+  <fixed>              Fixed slide image
+  <fixed-resolution>   Fixed image resolution (mm)
+  <reg-moving>         Moving timg from registration directory
+  <reg-fixed>          Fixed timg from registration directory (e.g. fixed4_nonlinear.timg)
+  <resampled-img>      Name for resampled output image
+
+optional arguments:
+  -h, --help           show this help message and exit
+  --inverse            Invert the transformation chain
+  ```
+
+For example:
+
+```shell
+slider_app.py APPLYXFM \
+    mr247MBP_c24_s20a.jp2 0.0004 \
+    mr247NeuN_c01_s19n.jp2 0.0004 \
+    mr247_mbp_to_neun.reg/moving.timg \
+    mr247_mbp_to_neun.reg/fixed4_nonlinear.timg \
+    m4247_mbp_to_neun.jp2
+```
+
+Or the inverse:
+
+```
+slider_app.py APPLYXFM \
+    mr247NeuN_c01_s19n.jp2 0.0004 \
+    mr247MBP_c24_s20a.jp2 0.0004 \
+    mr247_mbp_to_neun.reg/moving.timg \
+    mr247_mbp_to_neun.reg/fixed4_nonlinear.timg \
+    m4247_neun_to_mbp.jp2 \
+    --inverse
+```
+
+### Register chart to slide
+
+You can register a Neurolucida chart file to a 2D-slide using the `CHART` subcommand of the `slider_app.py` app.
+
+```shell
+>> slider_app.py CHART -h   
+usage: slider_app.py CHART [-h] [--out <dir>] <chart> <slide> <slide-resolution>
+
+Register charting to 2D slide
+
+positional arguments:
+  <chart>             Neurolucida chart file
+  <slide>             Fixed slide
+  <slide-resolution>  Slide image resolution (mm)
+
+optional arguments:
+  -h, --help          show this help message and exit
+  --out <dir>         Output directory 
+  ```
+
+For example:
+
+```shell
+slider_app.py CHART \
+    mr250NeuN_c14_s03.ASC \
+    mr250NeuN_c14_s03n.jp2 0.0004 \
+    --out=mr250_chart_to_neun.reg
+```
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