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README.md

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+
 # brainreg
 
 brainreg is an update to 
 [amap](https://github.com/SainsburyWellcomeCentre/amap-python) (itself a port 
 of the [original Java software](https://www.nature.com/articles/ncomms11879)) 
 to include multiple registration backends, and to support the many atlases 
-provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
+provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
+
+
+Documentation can be found [here](https://docs.cellfinder.info/brainreg/introduction).
+
+## Details
+The aim of brainreg is to register the template brain
+ (e.g. from the [Allen Reference Atlas](https://mouse.brain-map.org/static/atlas))
+  to the sample image. Once this is complete, any other image in the template
+  space can be aligned with the sample (such as region annotations, for 
+  segmentation of the sample image). The template to sample transformation
+  can also be inverted, allowing sample images to be aligned in a common 
+  coordinate space.
+
+To do this, the template and sample images are filtered, and then registered in 
+a three step process (reorientation, affine registration, and freeform 
+registration.) The resulting transform from template to standard space is then
+applied to the atlas. 
+
+Full details of the process are in the 
+[original aMAP paper](https://www.nature.com/articles/ncomms11879).
+![process](https://raw.githubusercontent.com/SainsburyWellcomeCentre/amap-python/master/resources/reg_process.png)
+**Overview of the registration process**
+
+## Installation
+```bash
+pip install brainreg
+```
+
+## Usage
+
+### Basic usage
+```bash
+brainreg /path/to/raw/data /path/to/output/directory -x 2 -y 2 -z 5
+```
+
+## Arguments
+### Mandatory
+
+* Path to the directory of the images. (Can also be a text file pointing to the files\)
+* Output directory for all intermediate and final results
+
+**You must also specify the pixel sizes, see [Specifying pixel size](https://docs.cellfinder.info/user-guide/usage/specifying-pixel-size)**
+
+### Additional options
+
+* `-d` or `--downsample` Paths to N additional channels to downsample to the same coordinate space.
+* `--sort-input-file` If set to true, the input text file will be sorted using natural sorting. This means that the file paths will be sorted as would be expected by a human and not purely alphabetically
+
+#### Misc options
+
+* `--n-free-cpus` The number of CPU cores on the machine to leave unused by the program to spare resources.
+* `--debug` Debug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues.
+
+### Atlas
+
+By default, brainreg will use the 25um version of the [Allen Mouse Brain Atlas](https://mouse.brain-map.org/). To use another atlas \(e.g. for another species, or another resolution\), you must use the `--atlas` flag, followed by the string describing the atlas, e.g.:
+
+```bash
+--atlas allen_mouse_50um
+```
+
+_To find out which atlases are available, once brainreg is installed, please run `brainglobe list`. The name of the resulting atlases is the string to pass with the `--atlas` flag._
+
+
+### Registration backend
+
+To change the registration algorithm used, use the `--backend` flag. The default is `niftyreg` as that is currently the only option.
+
+### Input data orientation
+
+If your data does not match the [brainglobe](https://github.com/brainglobe) default orientation \(the origin voxel is the most anterior, superior, left-most voxel, then you must specify the orientation by using the `--orientation` flag. What follows must be a string in the [bg-space](https://github.com/brainglobe/bg-space) "initials" form, to describe the origin voxel.
+
+
+
+If the origin of your data \(first, top left voxel\) is the most posterior, superior, left part of the brain, then the orientation string would be "psl" \(posterior, superior, left\), and you would use:
+
+```bash
+--orientation psl
+```
+
+
+### Registration options
+
+To change how the actual registration performs, see [Registration parameters](registration-parameters.md)
+
+Full command-line arguments are available with `brainreg -h`, but please 
+[get in touch](mailto:adam.tyson@ucl.ac.uk?subject=brainreg) if you have any questions.
+
+
+