diff --git a/README.md b/README.md index 11415ff2a92e9f7d7a9ca1d6fa5dcd4db8633e10..709312007f0fba5e9dcf73130d727e7cbde99c4f 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,28 @@ -# pointCloudUtilities +# PyNutil +PyNutil is a Python library for brain-wide quantification and spatial analysis of features in histological images from mouse and rat brain. It replicates the Quantifier feature of the Nutil software (RRID: SCR_017183), to be intergrated with the other QUINT workflow web-tools. It builds on registration to a standardised reference atlas with the QuickNII (RRID:SCR_016854) and VisuAlign software (RRID:SCR_017978) and feature extraction by segmentation with an image analysis software such as ilastik (RRID:SCR_015246). + +For more information about the QUINT workflow: +https://quint-workflow.readthedocs.io/en/latest/ +# Acknowledgements +PyNutil is developed at the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway with support from the EBRAINS infrastructure, and funding support from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA). + +# Authors and contributors +Harry Carey, Sharon C Yates, Gergely Csucs, Ingvild Bjerke, Rembrandt Bakker, Nicolaas Groeneboom, Maja A Punchades, Jan G Bjaalie. + +# Licence +- GNU General Public License v3 + +# Related articles +Yates SC, Groeneboom NE, Coello C, et al. & Bjaalie JG (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: 10.3389/fninf.2019.00075 + +Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG. Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 2020,14:37. https://doi.org/10.3389/fninf.2020.00037 + +Puchades MA, Csucs G, Lederberger D, Leergaard TB and Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796 + +Carey H, Pegios M, Martin L, Saleeba C, Turner A, Everett N, Puchades M, Bjaalie J, McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. BioRxiv. https://doi.org/10.1101/2022.04.28.489953 + +Berg S., Kutra D., Kroeger T., Straehle C.N., Kausler B.X., Haubold C., et al. (2019) ilastik:interactive machine learning for (bio) image analysis. Nat Methods. 16, 1226–1232. https://doi.org/10.1038/s41592-019-0582-9 + +# Contact us +Report issues here on Github or email: support@ebrains.eu