This dataset contains the raw images and templates from Cohort 2 (scanned once at three months, range PND74–110) of the manuscript:
Hanna Lemmik, Eugene Kim, Eilidh MacNicol, Davide Maselli, Michel Bernanos, Zhuoni Li, Dauda Abdullahi, Esther Walters, Maria Elisa Serrano Navacerrada, Wuding Zhou, Aleksandar Ivetic, Diana Cash, Laura Westacott, Complement receptor C3ar1 deficiency does not alter brain structure or functional connectivity across early life development, Brain Communications, 2025;, fcaf422, https://doi.org/10.1093/braincomms/fcaf422

Details related to access to the data

• Contact person

Hanna Lemmik — hannalemmik@hotmail.com, ORCID 0000-0002-2708-9557

Overview

• The project ran in though spring, summer and autumn 2023

• Brief overview of the tasks in the experiment

Anatomy and diffusion scans in vivo to locate synaptic pathology in C3ar1tm1Cge/C3ar1tm1Cge mouse model first reported in Humbles et al. (2000) Nature (https://doi.org/10.1038/35023175).

• Description of the contents of the dataset

C3ar1+/+ (wild type) N = 19, 11 males and 8 females; C3ar1tm1Cge/C3ar1tm1Cge N = 20, 11 males and 9 females.

Methods

See our paper doi: https://doi.org/10.1093/braincomms/fcaf422

Subjects

All animal procedures complied with the UK Animals and Scientific Procedures Act 1986 and were approved by the local ethical committee at King’s College London (KCL). Homozygous C3ar1-/- mice were generated by homologous recombination in embryonic stem cells and kindly provided by Dr. Bao Lu and Prof. Craig Gerard (Harvard Medical School, Boston, MA) (Humbles et al. 2000). These mice were subsequently backcrossed onto the C57BL/6J strain for at least 12 generations and maintained on a C57BL/6J background in Professor Wuding Zhou’s laboratory at KCL. For this study, cryopreserved stocks were rederived at KCL and crossed to C57BL/6J mice purchased from Charles River to refresh the genetic background following Jackson’s Laboratories line refreshing protocol.

Experimental animals (C3ar1-/- and C3ar1+/+ littermates) were generated through heterozygote incrosses and resulting genotypes followed Mendelian ratios. The heterozygote breeders were generated by outcrossing heterozygous mice to bought wild-type Charles River C57BL/6Js. The breeders used to produce the experimental animals were derived either from the first, second or third of these outcrosses. Sibling crosses were not conducted, and parental age was between 2–4 months to minimise genetic drift.

Experimental mice were housed in individually ventilated cages under controlled temperature (20–25°C), humidity (50–60%), and a 12-hour light-dark cycle (lights on at 7:00 AM, lights off at 7:00 PM). Environmental enrichment included nesting materials, tunnels, and chew sticks. Mice had ad libitum access to irradiated rodent chow and autoclaved water. Animals were group-housed (2–4 mice per cage), with males and females housed separately after weaning (PND21±2). Genotyping was conducted on ear biopsy DNA by Transnetyx using probes targeting the neomycin cassette for the mutant allele and intron 1 for the wild-type allele. No mismatches were identified through double-genotyping 20% of the study cohorts.

Apparatus

Mice were imaged using a Bruker BioSpec 9.4 T scanner with an 86-mm volume resonator for transmission and a 4-channel surface array coil. Anaesthesia was induced with 4% isoflurane in medical air (1 L/min) and oxygen (0.4 L/min), maintained at 2% but adjusted based on respiration rates. The respiration rate was monitored with a pressure sensor, and temperature was monitored with a rectal thermometer and maintained at 36–37°C using a water circulation system.

Additional data acquired

Open field, novel object recognition, elevated plus maze and prepulse inhibition tests were performed shortly before the adulthood scan.

The links for behaviour videos:

https://doi.org/10.5281/zenodo.17113949 (Cohort 2 novel object recognition training
and test videos).

https://doi.org/10.5281/zenodo.17113481 (Cohort 2 open field and elevated plus maze)

Experimental location

King's College London, BRAIN Centre

Key BRAIN Centre contacts: Diana Cash (Director): diana.cash@kcl.ac.uk Eugene Kim (Chief physicist): eugene.kim@kcl.ac.uk

https://openneuro.org/datasets/ds006670

Automated release for ds006663_2

Automated release for ds006663_1

This dataset contains the raw images and templates from Cohort 1 (scanned twice, once in adolescence between PND27-31 and once in adulthood between PND81–92) of the manuscript:
Hanna Lemmik, Eugene Kim, Eilidh MacNicol, Davide Maselli, Michel Bernanos, Zhuoni Li, Dauda Abdullahi, Esther Walters, Maria Elisa Serrano Navacerrada, Wuding Zhou, Aleksandar Ivetic, Diana Cash, Laura Westacott, Complement receptor C3ar1 deficiency does not alter brain structure or functional connectivity across early life development, Brain Communications, 2025; fcaf422, https://doi.org/10.1093/braincomms/fcaf422

Details related to access to the data

• Contact person

Hanna Lemmik — hannalemmik@hotmail.com, ORCID 0000-0002-2708-9557

Overview

The project ran though spring, summer and autumn 2023

Each mouse was scanned twice, once in adolescence between PND27-31 and once in adulthood between PND81–92
Adolescence: "PND30"
Adulthood: "PND90"

sessions.tsv included

• Brief overview of the tasks in the experiment

Anatomy and diffusion scans in vivo followed by BOLD rsfMRI to locate synaptic pathology in C3ar1tm1Cge/tm1Cge mouse model first reported in Humbles et al. (2000) Nature (https://doi.org/10.1038/35023175)

• Description of the contents of the dataset

C3ar1+/+ (wild type) N = 35, 17 males and 18 females; C3ar1tm1Cge/tm1Cge N = 34, 18 males and 16 females.

Methods

See our paper: https://doi.org/10.1093/braincomms/fcaf422

Subjects

All animal procedures complied with the UK Animals and Scientific Procedures Act 1986 and were approved by the local ethical committee at King’s College London (KCL). Homozygous C3ar1tm1Cge/tm1Cge mice were generated by homologous recombination in embryonic stem cells and kindly provided by Dr. Bao Lu and Prof. Craig Gerard (Harvard Medical School, Boston, MA) (Humbles et al. 2000). These mice were subsequently backcrossed onto the C57BL/6J strain for at least 12 generations and maintained on a C57BL/6J background in Professor Wuding Zhou’s laboratory at KCL. For this study, cryopreserved stocks were rederived at KCL and crossed to C57BL/6J mice purchased from Charles River to refresh the genetic background following Jackson’s Laboratories line refreshing protocol.

Experimental animals (C3ar1tm1Cge/tm1Cge and C3ar1+/+ littermates) were generated through heterozygote incrosses and resulting genotypes followed Mendelian ratios. The heterozygote breeders were generated by outcrossing heterozygous mice to bought wild-type Charles River C57BL/6Js. The breeders used to produce the experimental animals were derived either from the first, second or third of these outcrosses. Sibling crosses were not conducted, and parental age was between 2–4 months to minimise genetic drift.

Experimental mice were housed in individually ventilated cages under controlled temperature (20–25°C), humidity (50–60%), and a 12-hour light-dark cycle (lights on at 7:00 AM, lights off at 7:00 PM). Environmental enrichment included nesting materials, tunnels, and chew sticks. Mice had ad libitum access to irradiated rodent chow and autoclaved water. Animals were group-housed (2–4 mice per cage), with males and females housed separately after weaning (PND21±2). Genotyping was conducted on ear biopsy DNA by Transnetyx using probes targeting the neomycin cassette for the mutant allele and intron 1 for the wild-type allele. No mismatches were identified through double-genotyping 20% of the study cohorts.

Apparatus

Mice were imaged using a Bruker BioSpec 9.4 T scanner with an 86-mm volume resonator for transmission and a 4-channel surface array coil. We used a medetomidine and isoflurane anaesthesia optimised for mouse fMRI (Grandjean et al. 2014). This consisted of a subcutaneous medetomidine bolus (0.05 mg/kg) followed ten minutes later by its continuous infusion (0.1 mg/kg/h), with isoflurane levels gradually reduced to 0.45-0.65% over 15 minutes from the start of the infusion. BOLD fMRI was conducted after the structural scans, which took a further 45-60 minutes after reducing isoflurane level. The respiration rate was monitored with a pressure sensor (respiration remained between 100–160bpm), and temperature was monitored with a rectal thermometer and maintained at 36–37°C using a water circulation system.

Experimental location

King's College London, BRAIN Centre
Key BRAIN Centre contacts:
Diana Cash (Director): diana.cash@kcl.ac.uk
Eugene Kim (Chief physicist): eugene.kim@kcl.ac.uk

https://openneuro.org/datasets/ds006663

https://openneuro.org/datasets/ds005431

This dataset contains raw in vivo T2 weighted and single shell DWI images acquired from C58/J mice (a model of restricted, repetitive behavior) at 3-4 weeks postweaning following post-weaning exposure to either standard housing or environmental enrichment housing. Both female and male mice are included. MRI images were acquired using a Magnex Scientific 11.1 T scanner at the University of Florida's Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility. Additional study details are provided in the citation below.

Description: Effects of environmental enrichment on brain microstructure in C58 mice (juvenile cohort).

Please cite the following if you use these data:
Farmer, A. L., Febo, M., Wilkes, B. J., & Lewis, M. H. (2024). Environmental enrichment reduces restricted repetitive behavior by altering gray matter microstructure. PloS One, 19(7), e0307290.

Any publications using this data should acknowledge NIH grant S10 RR025671, which supported MRI/S instrumentation, as well as the McKnight Brain Institute at the National High Magnetic Field Laboratory’s Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, which is supported by National Science Foundation Cooperative Agreement DMR-1644779 and the State of Florida.

https://openneuro.org/datasets/ds005186

Resting state fMRI and dMRI data acquired on a cohort of 19 male F1 B6/129P mice (9-12 weeks).
https://openneuro.org/datasets/ds002307

Current available treatments for Parkinson s Disease (PD) focus on relieving motor and cognitive symptoms and improving quality of life. Animal models are essential to investigate PD aetiology, pathology, and therapeutic approaches. One of the most widely used PD animal models is the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse. Chronic injections with MPTP result in characteristics of PD in these animals including the loss of dopaminergic neurons, and gait and motor abnormalities. Because increased reactive oxidative stress is involved in the MPTP-induced neurotoxicity, the MPTP mouse model was selected with the aim of investigating the efficacy of ROS-redox modulating compound KH176 on behavioural deficits and structural- and functional brain connectivity caused by severe damage of the nigrostriatal dopaminergic system by administration of MPTP. In pursuing this goal, a behavioural, neuroimaging and neurobiological investigation has been carried out. Specifically, after having divided the animals in 4 experimental groups (compound or control diet and MPTP or vehicle injection), baseline and post-MPTP injection/diet treatment behavioural measurements were performed by using open field, rotarod, grip test, gait analysis and fear conditioning. Furthermore, animals were assessed with different brain imaging techniques to investigate brain structure and function, including dopamine transporter nuclear imaging (DAT-SPECT), resting state functional Magnetic Resonance Imaging (fMRI), and Diffusion Tensor Imaging (DTI). Animals were, then, sacrificed and blood plasma and brains were collected for molecular- and biochemical analysis and compound exposure. TH immunostaining was performed to quantify the dopaminergic neurons in the substantia nigra and striatum.

This dataset has been converted using BrkRaw (vmri_dho.json)at 2022-05-03 13:25:56.964953.

How to cite?

• https://doi.org/10.5281/zenodo.3818615

https://openneuro.org/datasets/ds005402

This dataset contains raw in vivo T2 weighted and single shell DWI images aquired from C58/J mice (a model of restricted, repetitive behavior) and C57BL/J mice at 6-7 weeks postweaning following post-weaning exposure to either standard housing or environmental enrichment housing. Both female and male mice are included. MRI images were acquired using a Magnex Scientific 11.1 T scanner at the University of Florida's Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility. Additional study details are provided in the citation below.

Description: Effects of environmental enrichment on brain microstructure in C58 mice (adult cohort).

Please cite the following if you use these data:

Any publications using this data should acknowledge NIH grant S10 RR025671, which supported MRI/S instrumentation, as well as the McKnight Brain Institute at the National High Magnetic Field Laboratory’s Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, which is supported by National Science Foundation Cooperative Agreement DMR-1644779 and the State of Florida.

https://openneuro.org/datasets/ds005236

This dataset contains MRI associated with the following publication, currently submitted to Stroke.

Title: Head down tilt 15° increases cerebral perfusion before recanalization in acute ischemic stroke due to large vessel occlusion. A pre-clinical MRI study
Authors: Simone Beretta, Davide Carone, Tae-Hee Cho, Martina Viganò, Susanna Diamanti, Jacopo Mariani, Francesco Pedrazzini, Elisa Bianchi, Cristiano Pini, Radu Bolbos, Marlene Wiart, Carlo Ferrarese, Fabien Chauveau
Preregistration: preclinicaltrials.eu, identifier PCTE0000198

Raw data:

MRI for 28 adult male Wistar rats (ILAR code Crl:WI(Han); RRID:RGD_2308816)
Magnetic field: 7T
Anesthesia: isoflurane
Time points (in hours, following occlusion): H0 (during MCA occlusion); H24 (after reperfusion)
Ethics statement: agreement numbers APAFIS#15529-2018061512184831v2 and 32924-2021091015062327v4 from local committee CELYNE-CNREEA (C2EA-42, Lyon, France)

Derivatives:

Time-to-Peak (TTP) maps calculated from DSC-PWI 
Matlab code used for TTP calculation
Excel files describing the experimental series and the main results

Notes:

No specification is available for Dynamic-Susceptibility-Contrast Perfusion-Weighted-Imaging (DSC-PWI), so the corresponding files are labelled in .bidsignore 
R10 had no anatomical T2w on H0
H24 session could not be performed for 8 animals  (R03-R10-R26-R28-R29-R31-R33-R34)
R28 was not positioned properly during the first run of DSC-PWI, positioning was corrected for the second run

This dataset has been converted using BrkRaw (v0.3.7) on 2024-01-23.

How to cite?

• https://doi.org/10.5281/zenodo.3818615

https://openneuro.org/datasets/ds004962