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

dataset
posted on 05.03.2021, 02:59 by Yuhan WangYuhan Wang, Mark Eddison, Greg Fleishman, Martin Weigert, Shengjin Xu, Fredrick E. Henry, Tim Wang, Andrew Lemire, Uwe Schmidt, Hui Yang, Konrad RokickiKonrad Rokicki, Cristian Goina, Karel SvobodaKarel Svoboda, Eugene W Myers, Stephan Saalfeld, Wyatt KorffWyatt Korff, Scott M. Sternson, Paul W. Tillberg

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).


Funding

HHMI Janelia Research Campus

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