epDevAtlas v1

The Early Postnatal Mouse Brain Developmental Atlas, Version 1.0 (epDevAtlas v1) is a suite of open access resources including 3D atlases of the early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Deposited in figshare is a collection of data used for the epDevAtlas v1 web platform, which can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 µm (XYZ in coronal plane). Average transformations were conducted at 20 µm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology. All 3D-counted cell types were registered to age-matched epDevAtlas templates and annotations.Ages included:Postnatal day (P) 4, 6, 8, 10, 12, 14, 56See README.txt forData ElementsAbbreviationsContents DescriptionLicenseConditions for UseCitation InformationSupportRelated LinksRelease Notes.Content OrganizationData folders are labeled by ageData files within each 'Age' folder are include age-matched Allen CCFv3 anatomical labels, reference brain template, and registered counted cell type data.Additional information in ReadMe fileConditions for UseThe epDevAtlas is a Brain Initiative Cell Census Network (BICCN) resource.BICCN data, tools, and resources, including the DevCCF are generally released under the Creative Commons Attribution 4.0 International Public License (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode) (“CC BY 4.0 License”). Under the CC BY 4.0 License external data users may freely download, analyze and publish results based on any BICCN open-access data and tools as soon as they are released, provided they give appropriate credit, a link to the license, and indicate if changes were made. The CC BY 4.0 License applies to all open-access datasets generated by individual members of the Network, regardless of type or size.Researchers using unpublished BICCN data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Network will continue to publish the results of its own analysis efforts in independent publications.Citation InformationPlease cite both the epDevAtlas manuscript in Nature Communications and this dataset if using the epDevAtlas in your work.We require that researchers who use BICCN datasets (published or unpublished) in any tools, web applications, presentations, and publications cite and acknowledge the BICCN and BICCN production laboratory(s) for referenced dataset(s).Release NotesepDevAtlas v1 (current release):This update is paired with the Liwang et al (2025) epDevAtlas manuscript in Nature Communications journal

早期出生后小鼠脑发育图谱（Early Postnatal Mouse Brain Developmental Atlas，版本1.0，简称epDevAtlas v1）是一套开放获取资源，包含早期出生后发育中小鼠脑的三维图谱以及经映射的细胞类型密度生长图表，既可作为独立资源使用，亦可用于实现数据集成。figshare平台存储了用于epDevAtlas v1网页平台的全套数据，可用于三维可视化分析γ-氨基丁酸能（GABAergic）、小胶质细胞（microglial）以及皮层层特异性细胞类型密度的时空生长特征。
经形态学平均的对称模板脑作为基础参考空间与坐标系，其各向同性分辨率为20 µm（冠状面XYZ轴方向）。本数据集以出生后（P）第4、6、8、10、12及14天的Vip-IRES-Cre;Ai14小鼠的高分辨率连续双光子断层扫描图像为基础，通过插值以20 µm体素分辨率完成平均变换。
针对所有年龄阶段的样本，研究人员以艾伦小鼠脑通用坐标框架（Allen CCFv3，P56）中的解剖学标签为基准，通过非线性迭代配准的方式将其映射至每个早期出生后时间点的模板，配准过程借助三维地标手动分区完成，且与艾伦小鼠参考图谱本体论（Allen Mouse Reference Atlas Ontology）保持一致。所有经三维计数的细胞类型均配准至与年龄匹配的epDevAtlas模板与注释信息中。本数据集涵盖的年龄阶段包括：出生后第4、6、8、10、12、14及56天（P4至P56）。
详见README.txt文件，可获取数据元素、缩写词、内容说明、许可协议、使用条款、引用信息、技术支持、相关链接以及更新日志等内容。
### 数据组织方式
数据文件夹按年龄进行命名。每个「年龄」文件夹内包含与对应年龄匹配的Allen CCFv3解剖学标签、参考脑模板以及经配准的细胞计数数据。更多信息详见README文件。
### 使用条款
epDevAtlas属于脑计划细胞普查网络（Brain Initiative Cell Census Network，BICCN）的资源。BICCN的各类数据、工具及资源（包括DevCCF）通常采用知识共享署名4.0国际公共许可协议（Creative Commons Attribution 4.0 International Public License，简称CC BY 4.0，https://creativecommons.org/licenses/by/4.0/legalcode）进行发布。
根据CC BY 4.0许可协议，外部数据使用者可在BICCN的开放获取数据与工具发布后，自由下载、分析并基于其发布研究成果，但需注明恰当的来源、提供许可协议链接，并说明是否对原始数据进行了修改。
CC BY 4.0许可协议适用于该网络成员所生成的所有开放获取数据集，无论其类型与规模大小。对于使用未公开BICCN数据的研究人员，本数据集鼓励其联系数据生产者以商讨协同发表事宜，但该步骤并非强制要求。该网络将继续以独立出版物形式发布其自身分析工作的相关成果。
### 引用说明
若在研究工作中使用epDevAtlas，请同时引用发表于《自然-通讯》（Nature Communications）的epDevAtlas相关论文与本数据集。对于在各类工具、网页应用、演示文稿及出版物中使用BICCN数据集（无论是否已公开）的研究人员，需引用并致谢提供相关数据集的BICCN及其制作实验室。
### 更新日志
当前发布版本为epDevAtlas v1。本次更新与2025年发表于《自然-通讯》的Liwang等人撰写的epDevAtlas相关论文配套发布。