Examples — starfish documentation

Examples¶

Examples of processing data with starfish

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Feature Identification¶

../_images/sphx_glr_plot_tissue_specific_corrections_thumb.png

Tissue Corrections¶

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Image Registration¶

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Image Corrections¶

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Loading ImageJ ROI Sets¶

../_images/sphx_glr_plot_image_manipulations_thumb.png

Image Manipulations¶

../_images/sphx_glr_normalize_intensity_values_thumb.png

Normalizing Intensity Values¶

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Pixel-Based Decoding¶

../_images/sphx_glr_ilastik_segmentation_thumb.png

Using ilastik in starfish¶

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Assigning Spots to Cells¶

../_images/sphx_glr_normalize_intensity_distributions_thumb.png

Normalizing Intensity Distributions¶

../_images/sphx_glr_spotbased_decoding_thumb.png

Spot-Based Decoding¶

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Watershed Segmentation¶

Quick Start¶

Tutorial introducing first-time users to a full starfish pipeline.

../_images/sphx_glr_plot_quick_start_thumb.png

Data Formatting¶

This section provides several examples of how to format data into SpaceTx-Format from a variety of types of input data shapes and sizes, demonstrating the flexibility of TileFetcher.

../_images/sphx_glr_plot_format_structured_data_thumb.png

Format Structured Data¶

../_images/sphx_glr_format_baristaseq_thumb.png

Format BaristaSeq¶

../_images/sphx_glr_format_iss_data_thumb.png

Format In Situ Sequencing Mouse x Human Experiment¶

../_images/sphx_glr_format_iss_breast_data_thumb.png

Format In-Situ Sequencing Data¶

../_images/sphx_glr_format_imc_data_thumb.png

Format Imaging Cytof Data¶

../_images/sphx_glr_format_merfish_U2OS_data_thumb.png

Format MERFISH data¶

../_images/sphx_glr_format_seqFISH_thumb.png

Format SeqFISH Data¶

../_images/sphx_glr_format_osmfish_thumb.png

Format osmFISH Data¶

../_images/sphx_glr_format_starmap_thumb.png

Format STARmap data¶

Advanced Data Loading¶

Advanced data loading techniques allow for users to directly load data from any file format into starfish.

../_images/sphx_glr_plot_tilefetcher_loader_thumb.png

Loading Data through TileFetchers¶

Example Pipelines¶

This section provides several examples of how to apply starfish to data from a variety of assay types assuming your data is already in spaceTx format.

../_images/sphx_glr_iss_pipeline_thumb.png

ISS Processing Workflow¶

../_images/sphx_glr_3d_smFISH_thumb.png

Single Field of View for sequential single-molecule FISH processed in 3d¶

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