What is CLARITY?
CLARITY imaging is a brain imaging technique which uses chemical compounds to capture detailed images of neuronal networks and other anatomical features.
CLARITY is a relatively new brain imaging technique, so finding an public CLARITY imaging dataset is quite a challenge. Luckily, there is one publicly available dataset, which we will be using in this tutorial.
The data we are using can be found here.
In particular, we will be the Tyrosine Hydroxylase (TH) stained mouse brain (z-stack). This file contains a mouse brain stained via the CLARITY imaging method.
You will also need ImageJ as well to process the CLARITY image data.
Once you have downloaded the data file and ImageJ, import the TIFF image data as a stack sequence using ImageJ.
To do this, open ImageJ and then click File -> Import -> Open Image Sequence
Once you have opened the TIFF files, convert them to a raw image file by clicking File -> Save As -> Raw Data.
Once your data is in a raw image format, we can import it to Paraview.
To import your raw image data in Paraview:
Click File -> Open and select your .raw file.
Then, under the properties menu, change the Data Scalar Type field to unsigned char and change the Data Extent field to [ [0, 2335], [0, 3243], [0, 99] ].
The Data Extent field describes the dimensions of our TIFF image stack and the Data Scalar Type field specifies how our data is stored.
Make sure to double check the properties of your data stack, otherwise you may run into errors such as:
CLARITY Images in ImageJ
CLARITY Images in Paraview
Colour Adjusted to Increase Contrast
Tutorial created by Ross Briden