Nutil simplifies the pre-and-post processing of images of sections from mouse and rat brain. It is a standalone application and requires no coding experience to execute. It is an integral part of the QUINT workflow.


Visit EBRAINS for more information about QUINT. Find user documentation here.

Nutil supports four 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. Quantifier: for the batch extraction, quantification and spatial analysis of labelling in mouse or rat brain sections (for example, immunohistochemical labelling).

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

Check out the following articles that have used Nutil:

  • 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.

  • Ham GX, Augustine GJ. Topologically Organized Networks in the Claustrum Reflect Functional Modularization. Frontiers in Neuroanatomy. 16 June 2022.

  • 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.

  • 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

  • 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.

  • 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: 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:

  • 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.