Examples — starfish documentation

Examples¶

Quick Start¶

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

../_images/sphx_glr_plot_quick_start_thumb.png

Tutorials¶

Tutorials for the image processing steps that construct a starfish pipeline

../_images/sphx_glr_plot_feature_identification_and_annotation_thumb.png

Feature Identification¶

../_images/sphx_glr_plot_tissue_specific_corrections_thumb.png

Tissue Corrections¶

../_images/sphx_glr_plot_image_registration_thumb.png

Image Registration¶

../_images/sphx_glr_plot_image_corrections_thumb.png

Image Corrections¶

../_images/sphx_glr_manual_segmentation_thumb.png

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¶

../_images/sphx_glr_pixelbased_decoding_thumb.png

Pixel-Based Decoding¶

../_images/sphx_glr_ilastik_segmentation_thumb.png

Using ilastik in starfish¶

../_images/sphx_glr_assigning_spots_thumb.png

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¶

../_images/sphx_glr_watershed_segmentation_thumb.png

Watershed Segmentation¶

Data Formatting¶

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¶

Starfish pipelines tailored for image data generated by groups using various image-based transcriptomics assays. When adapting these examples for other data sets, be cognizant that pipelines must be designed for the imaging system properties, sample characteristics, as well as the assay used.

../_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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