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@@ -1,6 +1,6 @@
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# Description of DAPI template
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-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 teamplate.
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+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.
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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.
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@@ -15,7 +15,8 @@ Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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- Download the and unzip the [example folder](./Example_folder.zip).
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- In a terminal window, navigate into the unzipped example folder.
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- Run the runner_example.sh with the command ```bash runner_example.sh```
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- - The automatically created segmentation can be found in ```Brain_example/Segmentation.nii```
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+ - The automatically created segmentation can be found in ```Brain_example/Segmentation.nii```.
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+ - To visualize the segmentation, open one of the channels ```Brain_example/im_c2.nii``` as main image and open the segmentation image ```Brain_example/Segmentation.nii``` as segmentation. Can for instance be done in [ITK-SNAP](http://www.itksnap.org/).
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For detailed parameter and output description go to the [automatic segmentation program](./automatic_segmentation_program).
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