******************************** MRI MOUSE BRAIN DATA OF ISCHEMIC LESION AFTER TRANSIENT MIDDLE CEREBRAL ARTERY OCCLUSION ******************************


																VERSION 1.0. JULY 2017
																
																
*********************************************************************** CITATION ***********************************************************************

If you use the data described here, please cite the following articles:

[1] I.A. Mulder, A. Khmelinskii, O. Dzyubachyk, S. de Jong, M.J.H. Wermer, M. Hoehn, B.P.F. Lelieveldt, A.M.J.M. van den Maagdenberg,
MRI mouse brain data of ischemic lesion after transient middle cerebral artery occlusion,
Frontiers in NeuroInformatics, 2017

[2] I.A. Mulder, A. Khmelinskii, O. Dzyubachyk, S. de Jong, N. Rieff, M.J.H. Wermer, M. Hoehn, B.P.F. Lelieveldt, A.M.J.M. van den Maagdenberg,
Automated ischemic lesion segmentation in MRI mouse brain after transient middle cerebral artery occlusion,
Frontiers in NeuroInformatics, 2017; 11(3)
http://doi.org/10.3389/fninf.2017.00003


*********************************************************************** CONTENTS ***********************************************************************

All files are consistently named. Names of the folders, subfolders and files are self-explanatory. In the _BRUKER_Folders the data are further subdivided
 into the age groups. In the _MHD_ folders all different age groups are in one same folder.
 
The original pulseprogram files of the Bruker folders were deleted. A folder containing the pulseprogram details is included: Pulseprogram_files.zip


Description of all the data can be found in the Frontiers in Neuroinformatics DATA REPORT article [1].

Description of the method used to produce the segmentations (automated and semi-automated) can be found in the Frontiers in Neuroinformatics ORIGINAL RESEARCH article [2].


Uploaded files:

READ_ME.txt (this file)

Cologne-Set-1.zip

Cologne-Set-2.zip

Leiden-Set_T2maps_Segmentations.zip

3-5month_old_mice_PART_1.zip

3-5month_old_mice_PART_2.zip

3-5month_old_mice_PART_3.zip

12-14month_old_mice.zip

20-24month_old_mice.zip

LS_MHD_echoes_PART_1.zip

LS_MHD_echoes_PART_2.zip

Pulseprogram_files.zip

Template_Dataset_and_Labels.zip


Instructions:

1. Extract '3-5month_old_mice_PART_1.zip', '3-5month_old_mice_PART_2.zip', '3-5month_old_mice_PART_3.zip' and merge them together into the '3-5month_old_mice' folder

2. Extract '12-14month_old_mice.zip' and '20-24month_old_mice.zip'

3. Move '3-5month_old_mice', '12-14month_old_mice' and '20-24month_old_mice' folders into the 'LS_BRUKER_Folders' folder

4. Extract 'LS_MHD_echoes_PART_1.zip', 'LS_MHD_echoes_PART_2.zip' and merge them together into the 'LS_MHD_echoes' folder

5. Extract 'Leiden-Set_T2maps_Segmentations.zip' and move the extracted folders ('LS_ImageJ_Manual_Segmentations_IAM', 'LS_ImageJ_Manual_Segmentations_SdJ', 
	'LS_MHD_Automated_Segmentations', 'LS_MHD_Manual_Segmentations_IAM', 'LS_MHD_Manual_Segmentations_SdJ', 'LS_MHD_T2maps'),
	together with the 'LS_MHD_echoes' and 'LS_BRUKER_Folders' folders, into the 'Leiden-Set' folder


Final main folders and subfolders structure:

Cologne-Set-1

	CS1_BRUKER_Folders
		3month_old_mice
	CS1_ImageJ_Manual_Segmentations_IAM
	CS1_ImageJ_Manual_Segmentations_SdJ
	CS1_MHD_Automated_Segmentations
	CS1_MHD_echoes
	CS1_MHD_Manual_Segmentations_IAM
	CS1_MHD_Manual_Segmentations_SdJ
	CS1_MHD_T2maps

Cologne-Set-2

	CS2_ImageJ_Manual_Segmentations_IAM
	CS2_ImageJ_Manual_Segmentations_SdJ
	CS2_MHD_Automated_Segmentations
	CS2_MHD_echoes
	CS2_MHD_Manual_Segmentations_IAM
	CS2_MHD_Manual_Segmentations_SdJ
	CS2_MHD_T2maps
	CS2_BRUKER_Folders
		2month_old_mice
		12month_old_mice

Leiden-Set

	LS_ImageJ_Manual_Segmentations_IAM
	LS_ImageJ_Manual_Segmentations_SdJ
	LS_MHD_Automated_Segmentations
	LS_MHD_echoes
	LS_MHD_Manual_Segmentations_IAM
	LS_MHD_Manual_Segmentations_SdJ
	LS_MHD_T2maps
	LS_BRUKER_Folders
		3-5month_old_mice
		12-14month_old_mice
		20-24month_old_mice

Pulseprogram_files

Template_Dataset_and_Labels


*********************************************************************** CONTACT ***********************************************************************

Oleh Dzyubachyk

Division of Image Procesing,
Department of Radiology, 
Leiden University Medical Center,
Leiden, the Netherlands
      
e-mail: o.dzyubachyk@lumc.nl