EASI-FISH reveals spatial and axonal projection patterns of molecularly defined cell types in the central amygdala (CEA)

We combined Expansion-Assisted Iterative Fluorescence in situ hybridization (EASI-FISH) with retrograde tracer labeling to reveal the spatial and axonal projection patterns of molecularly defined neuronal types in the central amygdala (CEA).  Here, 29 marker-genes were measured with EASI-FISH in 100µm thick brain slices in the mouse CEA, after retrograde tracer labeling in 5 downstream brain targets: the bed nucleus of the stria terminalis (BNST), lateral substantia nigra (lateral SN), periaqueductal gray   (PAG), parabrachial nucleus (PBN), and parvocellular reticular formation (PCRt).  'CEA_mFISH_data.csv' contains spot count for all marker genes, axonal projections, spatial locations (z, y, x) and cell body size (area) and shape (solidity), and cell_cluster for each neuron. Each row represents measurement from one neuron. Data collected in six samples from two animals are included here. </p

EASI-FISH example data (multi-round FISH, round 4)

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 datasets (multi-round FISH, round 3 and round 5) (https://doi.org/10.25378/janelia.13622819; https://doi.org/10.25378/janelia.13622828) for registration testing. LHA3_R4_small (12GB): Two image tiles are included in a single CZI file, with 2 channels (1 FISH channel and 1 DAPI channel). Channel1: 488 (Calb2), channel 2: 405 (DAPI) and image dimension per tile: 1920 x 1920 x 413 (x, y, z). </p