Automatic Rodent Segmentation Tools and Papers

Year	1st Author	Title	Data	Method
2020	J.M. Valverde	RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation (paper) (tool)	916 T2 Rats	Deep Learning
2019	J.M. Valverde	Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks (paper)	131 T2 Rats	Deep Learning
2018	A. Arnaud	Fully automatic lesion localization and characterization: Application to brain tumors using multiparametric quantitative MRI data (paper)	53 ADC, T1, T2, CBV, AUC Rats	Mixture Models
2018	C.H. Choi	A novel voxel-wise lesion segmentation technique on 3.0-T diffusion MRI of hyperacute focal cerebral ischemia at 1 h after permanent MCAO in rats (paper)	31 DWI Rats	Thresholding
2017	I.A. Mulder	Automated ischemic lesion segmentation in MRI mouse brain data after transient middle cerebral artery occlusion (paper) (tool)	121 T2 Mice	Level-sets

Year	1st Author	Title	Data	Method
2021	R. De Feo	Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases (paper) (tool)	1782 T2 Mice	Deep Learning
2016	M. Pagani	Semi-automated registration-based anatomical labelling, voxel based morphometry and cortical thickness mapping of the mouse brain (paper)	18 T2 Mice	Atlas
2014	D. Ma	Automatic structural parcellation of mouse brain MRI using multi-atlas label fusion (paper)	12+5 T2 Mice	Atlas

Year	1st Author	Title	Data	Method
2021	R. De Feo	Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases (paper) (tool)	1782 T2 Mice	Deep Learning
2020	Y. Liu	Automatic Brain Extraction for Rodent MRI Images (paper) (tool)	10 T1 Rats, 7 T2 Rats, 12 T1 Mice, 9 T2 Mice	Regional Blobs Combination
2018	S. Roy	A deep learning framework for brain extraction in humans and animals with traumatic brain injury (paper)(tool)	26 T1/T2 Mice	Deep Learning
2014	I. Oguz	RATS: Rapid Automatic Tissue Segmentation in Rodent Brain MRI (paper) (tool)	22 T1 Rats, 12 T2 Mice	Graph
2013	J. Li	An automatic rat brain extraction method based on a deformable surface model (paper)	64 T2 Rats	Deformable Surface
2013	T.C. Wood	rBET: making BET work for rodent brains (paper)(tool)	?? T1 Rats, T2 Mice	Deformable Surface
2011	N. Chou	Robust automatic rodent brain extraction using 3-D pulse-coupled neural networks (PCNN) (paper)	10 T2 Mice	PCNN
2008	M. Murugavel	Automatic Cropping of MRI Rat Brain Volumes using Pulse Coupled Neural Networks (paper)	42 T2 Rats	PCNN