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theislab / nicheformer

Repository for Nicheformer: a foundation model for single-cell and spatial omics
BSD 3-Clause "New" or "Revised" License
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MERFISH mouse brain data #11

Open yehuicheng2002 opened 3 months ago

yehuicheng2002 commented 3 months ago

Hello, I was trying the MERFISH mouse brain data, but the data obtained through the yao et al. paper https://www.nature.com/articles/s41586-023-06812-z#data-availability is not the same as what you show in nicheformer/ notebooks/tokenisation/merfish_mouse_brain.ipynb as you show: annData object with n_obs × n_vars = 4334174 × 550 obs: ‘brain_section_label’ var: ‘gene_symbol’, ‘transcript_identifier’ uns: ‘accessed_on’, ‘src’. You are showing this on the notebook:AnnData object with n_obs × n_vars = 4334174 × 483 obs: 'fov', 'volume', 'center_x', 'center_y', 'min_x', 'min_y', 'max_x', 'max_y', 'barcodeCount', 'corrected_x', 'corrected_y', 'origin', 'rotation', 'section', 'animal', 'merscope', 'target_atlas_plate', 'codebook', 'min_genes', 'min_total_reads', 'min_vol', 'genes_detected', 'total_reads', 'total_blanks', 'spot_density', 'max_blank_count', 'blanks_detected', 'cell_qc', 'best.cl', 'clean_region_label', 'prob', 'avg.dist', 'avg.path.cor', 'avg.cor', 'cor.zscore', 'cluster_id', 'cluster_label', 'supertype_id_label', 'Level2_id_label', 'Level1_id_label', 'class_id_label', 'cluster_id.AIT16', 'nt_type_label', 'luster_id', 'subclass_id_label', 'He.label', 'He.cor', 'class_label', 'division_label', 'division_id_label', 'subclass_label', 'supertype_label', 'nt_type_combo_label', 'CCF_landmark', 'CCF_bin_x', 'CCF_bin_y', 'CCF_bin_z', 'structures_id', 'CCF_acronym', 'CCF_analysis', 'CCF_broad', 'cell_type', 'in_fov', '_scvi_batch', '_scvi_labels', 'region', 'x', 'y', 'assay_ontology_term_id', 'organism_ontology_term_id', 'tissue_ontology_term_id', 'suspension_type', 'donor_id', 'condition_id', 'tissue_type', 'library_key', 'author_cell_type', 'niche', 'nicheformer_split', 'assay', 'organism', 'tissue', 'dataset'

What did you do with this part of the data to get the author_cell_type,to get the niche. Could you please share your correct download link?

Thank you very much！

Bunnyfcc commented 2 months ago

Hi, I have the same problem.Have you solved it yet?

yehuicheng2002 commented 2 months ago

Hi, I have the same problem.Have you solved it yet? No,I didn't.I try other data,without these labels