Python for Bioimage Analysis Example Dataset

HeLa cell confocal microscopy dataset (3-channel Z-stack, .czi) Short description: This dataset contains a confocal laser scanning microscopy image acquired on a Zeiss LSM 880 with AxioObserver microscope using a Plan-Apochromat 40x/1.3 Oil DIC UV-IR M27 objective. The sample consisted of HeLa cells stained with multiple fluorophores and mounted in prolong diamond. The .czi file includes a 3-channel fluorescence Z-stack (14 optical sections, 512 × 512 pixels per plane) with a voxel size of approximately 0.415 µm × 0.415 µm × 1 µm. Acquisition was performed in laser scanning confocal mode, with oil immersion and epifluorescence detection. Channels and dyes: Channel 1 – Alexa Fluor 568, mitochondria (anti-TOM20 primary antibody). Channel 2 – Alexa Fluor 488, microtubules (anti-tubulin primary antibody). Channel 3 – DAPI, nuclear staining. The dataset is meant to be used for training, benchmarking, and teaching in bioimage analysis, for tasks such as 3D cell segmentation and fluorescence quantification. Image specifications: File format: Zeiss CZI Image dimensions: 512 × 512 × 14 voxels Regions of interest: 4 Pixel type: 16-bit unsigned integer (12 effective bits per pixel) Channels: 3 fluorescence channels Timepoints: 1 Voxel size: 0.415 µm (X, Y), 1.0 µm (Z)