What is Nutil?

Nutil is a standalone desktop application for analysis of histological brain section images from mouse and rat using the QUINT workflow. It can be used to prepare images for analysis (TiffCreator, Transform, Resize) and to perform brain-wide quantification using a reference brain atlas (Quantifier).

Nutil allows four key operations:

  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: used as part of the QUINT workflow for the batch extraction, quantification and spatial analysis of labelling in mouse or rat brain sections using a reference brain atlas.

Tip

Visit EBRAINS for more information about QUINT.

Which atlases are supported?

Nutil supports analysis using the following brain atlases:

  • Allen Mouse Brain Atlas Common Coordinate Framework version 3 (CCFv3) (delineations from 2017 or 2015).

  • Waxholm Atlas of the Spraque Dawley Rat (WHS) (version 2, 3 and 4).

  • Kim Unified Adult Mouse Brain Atlas (version 1, 2019).

  • Developmental Mouse Brain Atlas for ages P4-P56 (DeMBA) with Allen CCFv3 delineations from 2017.

  • Developmental Mouse Brain Atlas for ages P4-P56 (DeMBA) with Kim Lab developmental delineations (KimLabDev CCFv001).

  • It is also possible to use other atlases using the “custom atlas” feature as long as they are integrated in the other QUINT tools (contact us at EBRAINS support to find out more).

Warning

While the Kim Unified and Developmental Mouse Brain Atlases are integrated in Nutil v1.0, a bug in this version (see release notes) means it is often best to use Nutil v0.8 for these atlases, with the atlases loaded via the “custom atlas” feature (see using a custom atlas).

The Allen Mouse Brain Atlas and Waxholm Atlas of the Sprague Dawley Rat Atlas are fully integrated in all versions of Nutil.

What is the output of Nutil?

TiffCreator: TiffCreator produces tiled TIFF files from JPEG, PNG and standard TIFF images.

Transform: Transform enables rotations, scaling and thumbnail compilation of large tiff files (currently up to 4GB) with output in tiff format.

Quantifier: Quantifier identifies individual objects in a segmented PNG file, while matching these to output from QuickNII/VisuAlign. The method first finds and sorts objects by using a standard pixel filler routine. Afterwards, a random object pixel is chosen as the look-up in the binary QuickNII/VisuAlign atlas slice for this particular image. When all objects have been assigned a region ID, multiple selections of predefined objects IDs are assembled, and finally output reports are created and written to disk. The output are as follows:

  1. Reports with counts and area fraction per reference atlas region (.CSV format).

  2. Reports with counts and area fraction per custom atlas region (custom regions are compilations of reference atlas regions) (.CSV format)

  3. Images with the segmentations superimposed on the atlas maps (.PNG format).

  4. Point clouds for visualising the extracted features using the 3D MeshView Atlas Viewer (.JSON format).

Learn more

Check out the following articles that have used Nutil as part of the QUINT workflow:

  • Yao Y, Barger Z, Saffari Doost M, Tso CF, Darmohray D, Silverman D, Liu D, Ma C, Cetin A, Yao S, Zeng H, Dan Y. Cardiovascular baroreflex circuit moonlights in sleep control. Neuron. 2022 Sep 23:S0896-6273(22)00802-9. https://doi.org/10.1016/j.neuron.2022.08.027.

  • Ham GX, Augustine GJ. Topologically Organized Networks in the Claustrum Reflect Functional Modularization. Frontiers in Neuroanatomy. 16 June 2022. https://doi.org/10.3389/fnana.2022.901807

  • Bjerke IE, Cullity ER, Kjelsberg K, Charan KM, Leergaard TB, Kim JH. DOPAMAP, high-resolution images of dopamine 1 and 2 receptor expression in developing and adult mouse brains. Sci Data. 2022 Apr 19;9(1):175. https://doi.org/10.1038/s41597-022-01268-8

  • Tocco C, Øvsthus M, Bjaalie J.G, Leergaard T.B and Studer M. Topography of corticopontine projections is controlled by postmitotic expression of the area-mapping gene Nr2f1. bioRxiv - May 2021 https://doi.org/10.1101/2021.05.10.443413

  • Kim S, Jo Y, Kook G, Pasquinelli C, Kim H, Kim K, Hoe HS, Choe Y, Rhim H, Thielscher A, Kim J, Lee HJ. Transcranial focused ultrasound stimulation with high spatial resolution. Brain Stimul. 2021 Mar-Apr;14(2):290-300. https://doi.org/10.1016/j.brs.2021.01.002

  • Whilden CM, Chevée M, An Seong Yeol, Pezon Brown S. The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse. J Comp Neurol. 2021 Dec;529(17):3751-3771. doi: https://doi.org/10.1002/cne.25163. Epub 2021 May 6.

  • McDonald MW, Jeffers MS, Filadelfi M, Vicencio A, Heidenreich G, Wu J and Silasi G. Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration. eNeuro 16 July 2021, 8 (4) ENEURO.0216-21.2021; DOI: https://doi.org/10.1523/ENEURO.0216-21.2021

  • Bjerke IE, Yates SC, Laja A, Witter MP, Puchades MA, Bjaalie JG and Leergaard TB. Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. 2021, iScience.https://doi.org/10.1016/j.isci.2020.101906