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 images in the series for QuickNII alignment and ilastik segmentation.
The QuickNII and ilastik software have different input image size requirements. It is also important that the input images follow the prescribed naming convention.
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 histological images are downscaled in order to enable efficient processing. The pixel classification algorithm relies on input from manual user annotations of the training images, and the features ‒ intensity, edge and/or texture ‒ of the image pixels. The resizing factor is determined by trial and error, with a test run performed with ilastik on images of different sizes to determine the optimal resolution for segmentation. As an example, in Yates et al, 2019, the image were downscaled by a factor of 0.1 and 0.05 for cellular features and Alzheimer's plaques respectively (factor applies to image width).
Naming convention
For QUINT analysis, Nutil Quantifier quantifies objects extracted from segmentations and registers them to regions defined by customised atlas maps. To match segmentations and corresponding atlas maps together, Nutil Quantifier relies on a unique ID in the file name of both files.The ID should be unique to the particular brain section and 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).
Running the transformation
Consult the Nutil user manual for detailed procedure (lincluded in the Nutil package available for download at Nitrc.org)
