Image pre-processing with Nutil Transform
The Transform feature in the Nutil software enables image rotation, renaming, resizing and mirroring and is used to prepare the image series for QuickNII alignment and ilastik segmentation.
The image input size requirements for the QuickNII and ilastik software differ. Naming convention of files is important.
For QuickNII, the input requirements described in (Puchades et al., 2019) are:
24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.4000x4000 or 5000x3000 pixels), however QuickNII does not benefit from image resolutions exceeding the resolution of the monitor in use. For a standard FullHD or WUXGA display
(1920x1080 or 1920x1200 pixels) the useful image area is approximately 1500x1000 pixels,using a similar resolution ensures optimal image-loading performance.
For ilastik (Borg et al.2019), the resizing was performed in order to enable efficient processing. To clarify, the pixel classification algorithm relies on input from manual user annotations of training images, and the features ‒ intensity, edge and/or texture ‒ of the image pixels. In practice, a test run was performed with ilastik on images of different sizes to find the optimal resolution for segmentation, with a final resize factor of e.g 0.1 for cellular features, and a factor of 0.05 for series with larger features like Alzheimer plaques.
Naming convention:
The file names of the segmentation and atlas maps that correspond to a particular section must contain a unique ID in the format: sXXX.., with XXX.. representing the section number. The section number should reflect the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4th section starting with section 2).
Example: tg2345_MMSH_s001_segmentation.png
(It is fine to include a string of letters and numbers followed by the unique ID).
For running the QUINT analysis the segmentation files and the customized atlas maps need to match and therefore the segmentation files should follow the same naming format.
Running the transformation
Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
