Histology-Based Fiber Tracking


Histology-based fiber tracking uses only the histology images to carry out fiber tracking. 

DSI Studio (versions after 2021/10) implemented structural tensor analysis (Zhang, IEEEE TMI 35, 294-306 2016, Schurr, Science, 2021) and integrated whole slide image parallel processing (Yeh, et al. J Pathol Inform 2014,  5:1) so that the analysis can be applied to large histology images (e.g. > 10,000 by 10,000 pixels).

Step 1: Load Histology Images

The analysis can be applied to almost any kind of histology stain, including Nissl, Parvalbumin IHC (preferred), H&E. 

You may find samples images at Allen Brain Atlas website (find the download button to download the "Entire Image" at Image Downsampling at x2)

The histology images (presumably whole slide images) have to be in jpeg or tiff format. 

Step 2: Mask and Parameters

Load images in DSI Studio using [Step T2 Reconstruction] (switch file type to histology when browsing files)

A default mask will be created (shown on the right) and can be modified by clicking [Edit >>]. The holes in the masks can be eliminated using [Negate]+[Defragments]+[Negate]

The parameters include the following:

in-plane resolution (mm): specify the in-plane resolution of the histology in millimeter. This is optional information to get a reference for setting fiber tracking parameters.
downsample (iterations): specify the number of iteration to downsample images at the end of the information output. One iteration will increase the pixel spacing by twofold. Usually, the fiber orientations are exported at 3 iterations (8 times of the original pixel spacing)
raw image smoothing (iterations): specify the number of iteration for smoothing the raw histology image.  
tensor smoothing (iterations): specify the number of iteration for smoothing the calculated structural tensor.  

Click on [Run Reconstruction] to process data into a FIB file.

Step 3: Fiber Tracking

Open the FIB file in DSI Studio using [Step T3 Fiber Tracking] and click on [Step T3d][Fiber Tracking] to get fiber tracks

Refer to Fiber Tracking in DSI Studio about the tracking parameters.

The original jpg or tif image can be added using [Slices][Add Other Images].