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QI2lab / merfish3d-analysis

3D MERFISH data processing
BSD 3-Clause "New" or "Revised" License
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merfish3d-analysis

WARNING: alpha software. We are sharing this early in case it is useful to other groups. Please expect breaking changes. Examples of running the package are found in /Examples.

GPU accelerated post-processing for 3D MERFISH data generated using qi2lab microscopes. This package currently Linux only due to RAPIDS.AI package availabilty.

Installation

Create a python 3.10 environment using your favorite package manager, e.g. mamba create -n wf-merfish python=3.10

Activate the environment and install the GPU dependencies.

mamba activate wf-merfish
mamba install -c conda-forge -c nvidia -c pytorch -c rapidsai cupy cucim=24.08 pylibraft cudadecon cuda-version=12.5 cudnn cutensor nccl onnx onnxruntime pytorch torchvision 'pytorch=*=*cuda*'

Finally, repository using git clone https://github.com/QI2lab/wf-merfish and then install using pip install . or for interactive editing use pip install -e ..

qi2lab MERFISH zarr layout v0.2

file format - /project_root - /calibrations.zarr (calibration information) - .zattrs - (with blank codes) - (e.g. round 0 -> codebook bits 0,1) - (objective NA, channels used, etc...) - (used for hotpixel correction) - (calculated based on experiment metadata) - /polyDT (raw and processed image data for polyDT label) - /tile000 - /round0000.zarr - .zattrs - (z,y,x in microns) - (excitation, emission) - (z,y,x in microns) - (what bits are linked to this polyDT image) - (affine transform for world coordinate warping) - (origin rigid translation transform for world coordinate warping) - (spacing scale transform for world coordinate warping) - (optional: raw camera data) - (hot pixel, offset, and gain corrected data) - (deconvolved data) - /round0001.zarr - .zattrs - (z,y,x in microns) - (excitation, emission) - (z,y,x in microns) - (what bits are linked to this polyDT image) - (rigid registration for round 0 alignment in pixels) - (optional: raw camera data) - (hot pixel, offset, and gain corrected data) - (optical flow field for round 0 alginment in pixels) - (deconvolved, then rigid and deformable registration applied to warp back to round 0) - /roundNNNN.zarr - /tile001 - ... - /tileNNN - /readouts (raw and processed image data for readout bits) - /tile0000 - /bit00.zarr - .zattrs - (excitation, emission) - (z,y,x in microns) - (what polyDT round is bit corresponds to) - (optional: raw camera data) - (hot pixel, offset, and gain corrected data) - (corrected, then rigid and defromable registration applied to warp back to round 0) - (deconvolved, then rigid and deformable registration applied to warp back to round 0) - (ufish prediction applied to registered_decon_data) - /bit01.zarr - ... - /bitNN.zarr - /ufish_localizations (ufish spot predictions, can be useful for diagnostics) - /tile0000 - bit01.parquet - bitNN.parquet - /tile0001 - .... - /tileNNNN - /decoded (decoding results) - tile0000_decoded_features.parquet - ... - tileNNNN_decoded_features.parquet - all_tiles_filtered_decoded_features.parquet - /decoded_optimization (temporary files used during iterative optimizing for normalization factors) - tileNNNN_decoded_features.parquet - /fused (fused, down-sampled polyDT image) - /fused.zarr - Either one of: - (polyDT and readouts deconvolved, registered data fused at isotropic voxel spacing) - (polyDT deconvolved, registered data fused at isotropic voxel spacing) - /segmentation (segmentation and spots-to-cell assignment results) - /cellpose - cell_centroids.parquet (yx centroid for each cell in maximum Z projection of cellpose mask prediction) - cell_outlines.json (yx polygons for each cell in maximum Z projection of cellpose mask prediction) - /cellpose.zarr - (cellpose masks generated from maximum Z projection data in fused.zarr) - /baysor - baysor_filtered_genes.parquet (gene ID, global zyx position, cell assignment, and confidence for all tiles) - segmentation_polygons.json (yx polygons for each cell determined by Baysor. GeoJSON format.) - diagnostic outputs (see Baysor repository for explanations) - /mtx_output (mtx formatted output of genes assigned to cells)