Nutil

Note

Nutil user manual and download information. RRID:SCR_017183.

Warning

Nutil v0.7.0 and v0.8.0 are stable and validated with multiple ground truth datasets.

It is not recommended to use Nutil v0.4.0 - v0.6.0 as they contain bugs that lead to incorrect results in some of the reports.

Nutil v1 has a known bug, which means its not possible to select “area splitting = yes” in the GUI. Nutil v1 can still be used for correct calculation of counts (“area splitting = no”), but if “area splitting = yes” for correct calculation of regional loads is needed, please use Nutil v0.8.0.

See the release notes for more information.

Nutil is a pre- and post-processing toolbox for histological images. It is an integral part of the QUINT workflow, enabling image transformations, file format conversion and renaming of files in order to prepare images for the QuickNII and ilastik software. It also supports the final quantification step in the workflow. Nutil has four features:

  1. TiffCreator: convert JPEG, PNG and normal TIFF images to tiled TIFF format.

  2. Transform: rename, rotate, resize and compile thumbnails of large tiled TIFF images (typical microscopy output format).

  3. Resize: for resizing JPEG/PNG images with output in PNG format.

  4. Quantifier: for the batch extraction, quantification and spatial analysis of labelling in mouse or rat brain sections.

For detailed instructions on how to use Nutil and analyse results, please go to the Nutil user documentation.