pipeline-manifest.json

[
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyGraph.pdf",
		"description": "Spatial adjacency graph of cells and their connected neighbors.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-normalized_cell_outlines.csv",
		"description": "Cell outlines normalized for size; first column indicates the scaling factor. xy coordinates are pair indices of a total 100 points but with 200 columns",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrix.mtx",
		"description": "Sparse matrix output of cell adjacency matrix for minimal distance.",
		"edam_ontology_term": "EDAM_1.24.format_3916"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrix_avg.mtx",
		"description": "Sparse matrix output of cell adjacency matrix for average distance.",
		"edam_ontology_term": "EDAM_1.24.format_3916"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrixRowColLabels.txt",
		"description": "text file of row and column label for adjacency matrix.",
		"edam_ontology_term": "EDAM_1.24.data_3671"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_1_texture.csv",
		"description": "texture features for each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_boundaries_channel_covar.csv",
		"description": "covariance of cell boundary pixel intensities for all channels for each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_boundaries_channel_mean.csv",
		"description": "mean intensity of cell boundary pixels for each cell for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_boundaries_channel_total.csv",
		"description": "total intensity of cell boundary pixels for each cell for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_boundaries_cluster.csv",
		"description": "cluster identification for clustering cells by total intensity in cell boundary pixels.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_centers.csv",
		"description": "pixel coordinates of cell centers of each segmented cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_channel_covar.csv",
		"description": "covariance of cytoplasm pixel intensities for all channels of each cell (not including cell boundary, nucleus or nuclear bounday).",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_channel_meanAll.csv",
		"description": "mean intensity of pixel intensities for all parts of each cell for all channels.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_channel_mean.csv",
		"description": "mean intensity of cytoplasm pixels in each cell (not including cell boundary, nucleus or nuclear bounday) for all channels.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_channel_total.csv",
		"description": "total intensity of cytoplasm pixels in each cell (not including cell boundary, nucleus or nuclear bounday) for all channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_cluster.csv",
		"description": "cluster identification for clustering by total intensity in cytoplasm of each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_polygons_spatial.csv",
		"description": "image coordinates for outline of each segmented cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_shape.csv",
		"description": "size + shape cell shape coordinates.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_shape_normalized.csv",
		"description": "normalized (only shape) cell shape coordinates.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-channel_pca.ome.tiff",
		"description": "Content of the top 3 principal components in each pixel (Red=PC1,Green=PC2,Blue=PC3) output as an ometiff.",
		"edam_ontology_term": "EDAM_1.24.format_3727"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-channelPCA_summary.csv",
		"description": "top 3 PCA components and their explained variance in each channel in the image.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyCovarpercell_boundaries.png",
		"description": "covariance clusters for cell boundaries mapped back into the spatial location of each respective cell boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyCovarpercell.png",
		"description": "covariance clusters for cells (cytoplasm) mapped back into the spatial location of each respective cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyCovarpernuclei.png",
		"description": "covariance clusters for nuclei mapped back into the spatial location of each respective nucleus.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyCovarpernucleus_boundaries.png",
		"description": "covariance clusters for cell boundaries mapped back into the spatial location of each respective cell boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyMeansAll.png",
		"description": "mean intensity of all parts of the segmentation mask (cell, nucleus, cell boundary, nucleus boundary) clusters mapped back into the spatial location of each respective cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyMeanspercell_boundaries.png",
		"description": "mean intensity clusters for cell boundary mapped back into the spatial location of each respective cell boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyMeanspercell.png",
		"description": "mean intensity clusters for cells mapped back into the spatial location of each respective cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyMeanspernuclei.png",
		"description": "mean intensity clusters for cell boundary mapped back into the spatial location of each respective cell boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyMeanspernucleus_boundaries.png",
		"description": "mean intensity clusters for nucleus boundaries mapped back into the spatial location of each respective nucleus boundary",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyTexture.png",
		"description": "texture clusters mapped back into the spatial location of each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyTotalpercell_boundaries.png",
		"description": "total intensity clusters for cell boundaries mapped back into the spatial location of each respective cell boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyTotalpercell.png",
		"description": "total intensity clusters for cells (cytoplasm) mapped back into the spatial location of each respective cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyTotalpernuclei.png",
		"description": "total intensity clusters for nuclei mapped back into the spatial location of each respective nucleus.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbyTotalpernucleus_boundaries.png",
		"description": "total intensity clusters for nucleus boundaries mapped back into the spatial location of each respective nucleus boundary.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusterbytSNEAllFeatures.png",
		"description": "tSNE clusters for all the features used in SPRM mapped back into the spatial location of each respective cell.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_covariance_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell boundary covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_covariance_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell boundary covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_mean_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell boundary mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_mean_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell boundary mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_total_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell boundary total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_boundaries_total_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell boundary total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_cellshape_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell shape cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_covariance_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_covariance_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_mean_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_mean_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercells_cellshape_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell shape cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercells_texture_legend.pdf",
		"description": "largest 3 channel contributions in the image to each texture cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_texture_legend.csv",
		"description": "largest 3 channel contributions in the image to each texture cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_total_legend.csv",
		"description": "largest 3 channel contributions in the image to each cell total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_total_legend.pdf",
		"description": "largest 3 channel contributions in the image to each cell total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clustercell_tSNE_legend.csv",
		"description": "largest 3 channel contributions in the image to each tSNE cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiffclusteringsilhouetteScores.csv",
		"description": "silhouette scores for clustering using different subsets of features.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cluster_meanALLCH_legend.csv",
		"description": "largest 3 channel contributions in the image to each mean intensity of all parts of the segmentation mask (cell, nucleus, cell boundary, nucleus boundary) cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cluster_meanALLCH_legend.pdf",
		"description": "largest 3 channel contributions in the image to each mean intensity of all parts of the segmentation mask (cell, nucleus, cell boundary, nucleus boundary) cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_covariance_legend.csv",
		"description": "largest 3 channel contributions in the image to each nuclei covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_covariance_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nuclei covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_mean_legend.csv",
		"description": "largest 3 channel contributions in the image to each nuclei mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_mean_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nuclei mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_total_legend.csv",
		"description": "largest 3 channel contributions in the image to each nuclei total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternuclei_total_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nuclei total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_covariance_legend.csv",
		"description": "largest 3 channel contributions in the image to each nucleus boundary covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_covariance_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nucleus boundary covariance cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_mean_legend.csv",
		"description": "largest 3 channel contributions in the image to each nucleus boundary mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_mean_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nucleus boundary mean intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_total_legend.csv",
		"description": "largest 3 channel contributions in the image to each nucleus boundary total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-clusternucleus_boundaries_total_legend.pdf",
		"description": "largest 3 channel contributions in the image to each nucleus boundary total intensity cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-Cluster_Shape.png",
		"description": "clustering by cell shape mapped back onto the spatial locations of cells in the image.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_img_binary.png",
		"description": "foreground and background binarization of the image (used for evaluation of the segmentation).",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nuclei_1_texture.csv",
		"description": "nuclei texture ",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nuclei_channel_covar.csv",
		"description": "covariance of nuclear pixels for all channels for each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nuclei_channel_mean.csv",
		"description": "mean intensity of nuclei for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nuclei_channel_total.csv",
		"description": "total intensity of nuclei for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nuclei_cluster.csv",
		"description": "cluster identification for each nucleus.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nucleus_boundaries_channel_covar.csv",
		"description": "covariance of nuclear boundaries pixels for all channels for each cell.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nucleus_boundaries_channel_mean.csv",
		"description": "mean intensity of nuclear boundary pixels for each cell for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nucleus_boundaries_channel_total.csv",
		"description": "total intensity of nuclear boundary pixels for each cell for each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-nucleus_boundaries_cluster.csv",
		"description": "cluster identification for clustering by nuclear boundaries total intensity.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-SNR.csv",
		"description": "Signal to noise ratio of each channel image by otsu and z-score.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-SPRM_Image_Quality_Measures.json",
		"description": "Image Quality Measures.",
		"edam_ontology_term": "EDAM_1.24.format_3464",
		"is_qa_qc": true
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-superpixel.ome.tiff",
		"description": "Clustering of pixels by intensities in each channel written out as an ome.tiff.",
		"edam_ontology_term": "EDAM_1.24.format_3727"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-Superpixels.png",
		"description": "Clustering of pixels by intensities of each channel.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-Top3ChannelPCA.png",
		"description": "Content of the top 3 principal components in each pixel (Red=PC1,Green=PC2,Blue=PC3).",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-tSNE_allfeatures.csv",
		"description": "tSNE 2-Dimensional projection of all SPRM calculated features.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-tSNE_allfeatures.pdf",
		"description": "tSNE 2-Dimensional projection of all SPRM calculated features.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-Cluster_ShapeNormalized.png",
		"description": "clustering by normalized cell shape mapped back onto the spatial locations of cells in the image.",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cellshapenormalized_legend.pdf",
		"description": "largest 3 channel contributions in the image to each normalized cell shape cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cellshapenormalized_legend.csv",
		"description": "largest 3 channel contributions in the image to each normalized cell shape cluster.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_nmf_top3.png",
		"description": "dimensionality reduction by NMF (Non-Negative Matrix Factorization) on image",
		"edam_ontology_term": "EDAM_1.24.format_3603"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_nmf_components.csv",
		"description": "dimensionality reduction by NMF (Non-Negative Matrix Factorization) on image and their corresponding component values",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_nmf_components.pdf",
		"description": "dimensionality reduction by NMF (Non-Negative Matrix Factorization) on image and heat map visualization of their components",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_subtype.ome.tiff",
		"description": "subtype tiff image in which the channels represent the feature subtypes. The index of the channels correspond to the labels in the subtype labels csv.",
		"edam_ontology_term": "EDAM_1.24.format_3727"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_subtype_labels.csv",
		"description": "subtype labels where the index of the columns in the csv match corresponds with the index in the channels of the subtype tiff image.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	},
	{
		"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_subtype_scores.csv",
		"description": "The score assigned to each feature by the subtyping algorithm for best overlap of subtype and feature clusters.",
		"edam_ontology_term": "EDAM_1.24.format_3752"
	}
]