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.

Downloading Process

  • The data we are using can be found here.

  • 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