EASI-FISH example data (multi-round FISH, round 3)

Example dataset that can be used for testing the EASI-FISH (Expansion-Assisted Iterative Fluorescence in situ hybridization) data analysis pipeline (https://github.com/JaneliaSciComp/multifish). Raw image data (.czi) and metadata (.mvl) are provided here. Image data was collected using a Zeiss Lightsheet Z.1 microscope. A 20× water-immersion objective (RI=1.33) was used for imaging with 1× zoom. Single-side illumination was used to reduce light exposure and imaging time. Overlap between tiles was set to 8%. Voxel size (µm): 0.23 x 0.23 x 0.42 (x, y, z). This dataset can be used with EASI-FISH example data (multi-round FISH, round 5) (https://doi.org/10.25378/janelia.13622828) for registration testing. LHA3_R3_medium (32GB): Two image tiles are included in a single CZI file, with 4 channels (3 FISH channels and 1 DAPI channel). Channel1: 488 (Gpr83), channel 2: 669 (Slc17a6), channel 3: 405 (DAPI), channel 4: 546 (Bdnf) and image dimension per tile: 1920 x 1920 x 591 (x, y, z). LHA3_R3_small (12GB): Two image tiles are included in a single CZI file, with 2 channels (1 FISH channel and 1 DAPI channel). Channel1: 488 (Gpr83), channel 2: 405 (DAPI) and image dimension per tile: 1920 x 1920 x 422 (x, y, z). LHA3_R3_tiny (<1GB): Two image tiles are included in two separate CZI files (LHA3_R3_tiny_V01.czi and LHA3_R3_tiny_V02.czi), with 2 channels (1 FISH channel and 1 DAPI channel). Channel1: 488 (Gpr83), channel 2: 405 (DAPI). Please note that this set is for software testing only and the output from this set may not reflect the actual performance of the pipeline, which is optimized for large datasets.

搜集汇总

背景与挑战

背景概述

该数据集是用于测试EASI-FISH数据分析流程的示例数据，包含原始图像数据（.czi）和元数据（.mvl），使用Zeiss Lightsheet Z.1显微镜采集。数据集包含不同大小的图像文件，分别具有不同的通道和图像尺寸，适用于软件测试和大型数据集分析。