Update 'README.md'

README.md

@@ -1,10 +1,13 @@
 
+  
 # Description of DAPI template
 This repository contains a three-dimensional population-based average atlas, the DAPI template, of the C57BL/6 mouse brain stained with the commonly employed fluorescence nuclear stain DAPI. The [DAPI template](./data/dapi_template.nii.gz), [accompanying segmentation](./data/dapi_template_segmentation_full.nii.gz), and a [simplified segmentation](./data/dapi_template_segmentation_simple.nii.gz) can be found as nifti files in ```data/```. Moreover, the repository contains all the raw data (```data/mice/```) and the full code base (```template_creation_pipieline/```) which was used in the construction of the template.
 
 The DAPI template, is constructued from consecutive coronal brain slices of 12 male mice aged between 10-11 weeks. Each mouse brain is first reconstructed into a three-dimensional volume and then an iterative averaging process of these reconstructed brain volumes was employed to yield the final population-based average.
 
-The repository also includes an automatic segmentation/spatial normalization pipeline (```automatic_segmentation_program/```) for novel coronal slices described below. 
+The repository also includes an automatic segmentation/spatial normalization pipeline (```automatic_segmentation_program/```) for novel coronal slices described below.
+
+You can also find a [guide](#overlay-with-allenccf) on how to visualize the AllenCCF on top of the DAPI template.
 
 # Automatic slice segmentation
 
@@ -51,4 +54,29 @@ Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
 ## Usage  
 Use runner.py to preprocess and output a segmentation registred to the slice. For detailed parameter and output description go to the [automatic segmentation program](./automatic_segmentation_program).
 
-
+## Overlay with AllenCCF
+To visualize the Allen CCF on top of the DAPI template:
+
+ 1. Download the [DAPI template](./data/dapi_template.nii.gz).
+ 2. Download the current AllenCCF template in the desired resolution from the [download page](https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/).
+ 3. Download the [transformation](./ccf_to_dapi_affine_transformation.txt).
+ 4. Apply the transformation to the AllenCCF template. Using *average_template_25.nrrd* as  example, this can either be done with:
+
+**ANTs**:
+```
+TRANFORMATION=ccf_to_dapi_affine_transformation.txt
+antsApplyTransforms \
+ -i average_template_25.nrrd \
+ -d 3 \
+ -r dapi_template.nii.gz \
+ -o average_template_25_registered_to_dapi.nii.gz \
+ -t ${TRANSFORMATION}
+```
+
+**ITK-SNAP**
+
+ 1. Open the DAPI template (*dapi_template.nii.gz*) in ITK-SNAP
+ 2. Add the AllenCCF template (*average_template_25.nrrd*) as a seperate image (File->Add Another Image).
+ 3. Open Tools->Registration, which will open a panel to the right.
+ 4. In the bottom right, press the folder icon (*'Load transformation from file'*) and choose the transformation (*ccf_to_dapi_affine_transformation.txt*).
+ 5. If you want to save the transformed AllenCCF, press the reslice icon (*'Reslice the moving...'*) and choose *ok*. Now you have 3 small images in the top right corner of each plane. Press the bottom one, press the little drop-down in the small image, and choose *'save image'*.