Time-Lapse Microscopy of Cycling RPE1 Cells with Brightfield and H2B Imaging, Annotated with Cell Cycle States from integrated FUCCI Intensities

We acquired a high-resolution time-lapse fluorescence microscopy dataset of dividing human Fucci RPE1 cells, capturing images every 5 minutes. Cell nuclei were segmented using a custom StarDist model (Weigert and Schmidt) on an additional nuclear histone marker (H2B) channel and tracked across frames with TrackMate (Tinevez et al.) from 72-hour recordings. Full cell cycle tracks were identified through K-Means clustering, and ground-truth labels were derived by normalizing the average Fucci intensities per nucleus and applying a logarithmic transformation. The training dataset includes 5,188 complete cell cycle tracks (M-M), with each track containing two imaging modalities—Brightfield and H2B fluorescence—represented as 64×64 images centered on the nucleus. We also provide two independent test datasets: one with unperturbed control cells (358 complete tracks) and another with drug-treated cells exhibiting cell cycle abnormalities (73 complete tracks). We also included the model weights in the models.zip file. Imaging metadata: Images from four channels—Brightfield, H2B (far red), Cdt1 (red), and Geminin (green)—were acquired every 5 minutes using a PerkinElmer Operetta Microscope with a 20x/0.80 objective (wide-field microscopy). Four or nine tiles per well were captured for each channel, with a 15% overlap for subsequent stitching. In the images, 1 pixel equates to 0.5979761uM. The laser intensities and time of exposure for each channel are shown in the table below. Channel Laser Intensity Exposure time Fucci Green 25% 30 ms Fucci Red 15% 10 ms H2B Far Red 30% 30 ms Brightfield 50% 5 ms本研究采集了人类Fucci标记的RPE1细胞分裂过程的高分辨率延时荧光显微镜数据集，成像间隔为5分钟。本数据集基于72小时的连续成像记录，通过自定义StarDist模型（Weigert与Schmidt开发）对额外细胞核组蛋白标记物（H2B）通道图像进行细胞核分割，并借助TrackMate（Tinevez等开发）完成跨帧细胞追踪。通过K均值聚类识别完整细胞周期轨迹，并对每个细胞核的平均Fucci荧光强度进行归一化处理后施以对数变换，以此生成真值标签。 训练集包含5188条完整的M-M细胞周期轨迹，每条轨迹对应两种成像模态——明场（Brightfield）与H2B荧光图像，均为以细胞核为中心的64×64像素图像。此外还提供两组独立测试集：一组为未受干扰的对照细胞（含358条完整轨迹），另一组为经药物处理、表现出细胞周期异常的细胞（含73条完整轨迹）。 模型权重文件已打包至models.zip中。 成像元数据： 本数据集采用PerkinElmer Operetta显微镜搭配20×/0.80物镜（宽场成像），以5分钟为间隔采集四个通道的图像：明场、H2B（远红外）、Cdt1（红色）及Geminin（绿色）。每个孔道的每个通道采集4或9张图像瓦片（tiles），图像间重叠率为15%，用于后续拼接。图像中1像素对应0.5979761微米。各通道的激光强度与曝光时长如下表所示： 通道 激光强度 曝光时长 Fucci绿色通道 25% 30毫秒 Fucci红色通道 15% 10毫秒 H2B远红外通道 30% 30毫秒 明场通道 50% 5毫秒