OME-Zarr hiPSC 3D immunofluorescence images, tiny test set
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<em>This dataset is intended to be used for automated testing of OME-Zarr processing.</em> Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for Fractal: https://github.com/fractal-analytics-platform/fractal It is a subset of this dataset: https://zenodo.org/record/7057076 1 Channel is included: - C01: DAPI, nuclear stain This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000. The data was acquired in the Pelkmans lab in August 2020. The images have been processed using Fractal, the workflow is attached as a json file. It was run using this script to generate the workflow. It ran with fractal-server==1.3.1, fractal-client==1.3.0 and fractal-tasks-core==0.10.0. Two versions are added here: A 3D version with both Z planes. And a 2D version (MIP of the Z-planes) which also contains label images from cellpose segmentation.
本数据集旨在用于OME-Zarr处理的自动化测试。本数据集为人类诱导多能干细胞(human induced pluripotent stem cells)的示例数据集,采用40倍放大倍率拍摄,成像设备为Yokogawa CV7000。该数据集是某大型实验的极小子集,专门作为Fractal的测试数据集,其原始完整数据集源自:https://zenodo.org/record/7057076,Fractal项目仓库地址为:https://github.com/fractal-analytics-platform/fractal。本次子集仅包含1个成像通道:C01通道为DAPI,即细胞核染色剂。该单通道数据集包含2个视场的2层Z轴切片,同时附带经手动调整的Yokogawa CV7000成像系统元数据文件。本数据于2020年8月在Pelkmans实验室采集完成。图像已通过Fractal完成处理,处理工作流以JSON格式文件附随发布。该工作流通过对应脚本生成,运行时依赖的版本分别为:fractal-server==1.3.1、fractal-client==1.3.0及fractal-tasks-core==0.10.0。本次发布包含两个版本:其一为包含全部两层Z轴切片的3D版本;其二为基于Z轴切片最大强度投影(MIP)生成的2D版本,该版本同时附带由Cellpose细胞分割得到的标签图像。



