EASI-FISH example data (multi-round FISH, round 3)
收藏资源简介：
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.
本数据集可用于测试EASI-FISH（扩展辅助迭代荧光原位杂交，Expansion-Assisted Iterative Fluorescence in situ hybridization）数据分析流程（https://github.com/JaneliaSciComp/multifish）。此处提供原始图像数据（.czi格式）与元数据（.mvl格式）。 图像数据采用Zeiss Lightsheet Z.1显微镜采集，使用20×水浸物镜（折射率RI=1.33），成像倍率为1×。实验采用单侧照明以降低光暴露与成像时长，图像拼接区块的重叠率设置为8%。体素尺寸（单位：μm）为0.23×0.23×0.42（x、y、z轴）。 本数据集可搭配EASI-FISH示例数据（多轮荧光原位杂交，第5轮）（https://doi.org/10.25378/janelia.13622828）用于配准测试。 数据集包含三个子版本： 1. LHA3_R3_medium（32GB）：单个CZI文件中包含2个图像拼接区块，涵盖4个通道（3个FISH通道与1个DAPI通道）：通道1：488（Gpr83），通道2：669（Slc17a6），通道3：405（DAPI），通道4：546（Bdnf）；每个拼接区块的图像维度为1920×1920×591（x、y、z轴）。 2. LHA3_R3_small（12GB）：单个CZI文件中包含2个图像拼接区块，涵盖2个通道（1个FISH通道与1个DAPI通道）：通道1：488（Gpr83），通道2：405（DAPI）；每个拼接区块的图像维度为1920×1920×422（x、y、z轴）。 3. LHA3_R3_tiny（<1GB）：包含两个独立的CZI文件（LHA3_R3_tiny_V01.czi与LHA3_R3_tiny_V02.czi），每个文件中各含1个图像拼接区块，涵盖2个通道（1个FISH通道与1个DAPI通道）：通道1：488（Gpr83），通道2：405（DAPI）。 请注意，本数据集仅用于软件测试，由此得到的输出结果无法反映该流程的实际性能——该流程是针对大型数据集优化的。
