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

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