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04_marker_review
04_marker_review
 
 
05_distinct_palette_review
05_distinct_palette_review
 
 
CosMX_seg_test
CosMX_seg_test
 
 
marker_dotplots
marker_dotplots
 
 
notebook04_result
notebook04_result
 
 
pan-IKZF_celltyping_draft
pan-IKZF_celltyping_draft
 
 
.DS_Store
.DS_Store
 
 
00A_Check_and_Repair_Corrected_Source_Zarr.ipynb
00A_Check_and_Repair_Corrected_Source_Zarr.ipynb
 
 
00_TBIO8111_Config_Preflight.ipynb
00_TBIO8111_Config_Preflight.ipynb
 
 
00_TBIO8111_Config_Preflight_OpenSlide_tifffile_fallback.ipynb
00_TBIO8111_Config_Preflight_OpenSlide_tifffile_fallback.ipynb
 
 
01_TBIO8111_StarDist_QCprior_OpenSlide_tifffile_fallback.ipynb
01_TBIO8111_StarDist_QCprior_OpenSlide_tifffile_fallback.ipynb
 
 
03_TBIO8110_CellQC_ObsTransfer_CellCycle.ipynb
03_TBIO8110_CellQC_ObsTransfer_CellCycle.ipynb
 
 
06B_LungDev_RAPIDS_Harmony_Audit_CAGRA_v3_H5ADsafe _finished.ipynb
06B_LungDev_RAPIDS_Harmony_Audit_CAGRA_v3_H5ADsafe _finished.ipynb
 
 
06D_LungDev_RAPIDS_RawCounts_BackboneQC_RecurrentHVG_Harmony_run1.ipynb
06D_LungDev_RAPIDS_RawCounts_BackboneQC_RecurrentHVG_Harmony_run1.ipynb
 
 
Connect Robert Engagement .pptx
Connect Robert Engagement .pptx
 
 
D142_RLL_5B1_8_preliminary_celltype_HE_roi1_300dpi.png
D142_RLL_5B1_8_preliminary_celltype_HE_roi1_300dpi.png
 
 
D142_RLL_5B1_8_preliminary_celltype_HE_roi2_300dpi.png
D142_RLL_5B1_8_preliminary_celltype_HE_roi2_300dpi.png
 
 
D142_RLL_5B1_8_preliminary_celltype_HE_whole_300dpi.png
D142_RLL_5B1_8_preliminary_celltype_HE_whole_300dpi.png
 
 
D142_RLL_5B1_8_proseg_qcclass_boundaries_preview.png
D142_RLL_5B1_8_proseg_qcclass_boundaries_preview.png
 
 
D142_RLL_5B1_8_proseg_qcclass_boundaries_whole.png
D142_RLL_5B1_8_proseg_qcclass_boundaries_whole.png
 
 
D142_RLL_5B1_8_proseg_qcclass_qc_panels.pdf
D142_RLL_5B1_8_proseg_qcclass_qc_panels.pdf
 
 
D142_RLL_5B1_8_stardist_qc_center.png
D142_RLL_5B1_8_stardist_qc_center.png
 
 
D142_RLL_5B1_8_stardist_qc_overview.png
D142_RLL_5B1_8_stardist_qc_overview.png
 
 
D194_RLL_5A2_6_preliminary_celltype_HE_roi1_300dpi.png
D194_RLL_5A2_6_preliminary_celltype_HE_roi1_300dpi.png
 
 
D194_RLL_5A2_6_preliminary_celltype_HE_roi2_300dpi.png
D194_RLL_5A2_6_preliminary_celltype_HE_roi2_300dpi.png
 
 
D194_RLL_5A2_6_preliminary_celltype_HE_whole_300dpi.png
D194_RLL_5A2_6_preliminary_celltype_HE_whole_300dpi.png
 
 
D194_RLL_5A2_6_proseg_qcclass_boundaries_preview.png
D194_RLL_5A2_6_proseg_qcclass_boundaries_preview.png
 
 
D194_RLL_5A2_6_proseg_qcclass_boundaries_whole.png
D194_RLL_5A2_6_proseg_qcclass_boundaries_whole.png
 
 
D194_RLL_5A2_6_proseg_qcclass_qc_panels.pdf
D194_RLL_5A2_6_proseg_qcclass_qc_panels.pdf
 
 
D194_RLL_5A2_6_stardist_qc_center.png
D194_RLL_5A2_6_stardist_qc_center.png
 
 
D194_RLL_5A2_6_stardist_qc_overview.png
D194_RLL_5A2_6_stardist_qc_overview.png
 
 
D327_RLL_4A2_6_preliminary_celltype_HE_roi1_300dpi.png
D327_RLL_4A2_6_preliminary_celltype_HE_roi1_300dpi.png
 
 
D327_RLL_4A2_6_preliminary_celltype_HE_roi2_300dpi.png
D327_RLL_4A2_6_preliminary_celltype_HE_roi2_300dpi.png
 
 
D327_RLL_4A2_6_preliminary_celltype_HE_whole_300dpi.png
D327_RLL_4A2_6_preliminary_celltype_HE_whole_300dpi.png
 
 
D327_RLL_4A2_6_proseg_qcclass_boundaries_preview.png
D327_RLL_4A2_6_proseg_qcclass_boundaries_preview.png
 
 
D327_RLL_4A2_6_proseg_qcclass_boundaries_whole.png
D327_RLL_4A2_6_proseg_qcclass_boundaries_whole.png
 
 
D327_RLL_4A2_6_proseg_qcclass_qc_panels.pdf
D327_RLL_4A2_6_proseg_qcclass_qc_panels.pdf
 
 
D327_RLL_4A2_6_stardist_qc_center.png
D327_RLL_4A2_6_stardist_qc_center.png
 
 
D327_RLL_4A2_6_stardist_qc_overview.png
D327_RLL_4A2_6_stardist_qc_overview.png
 
 
D430_RLL_7A2_6_preliminary_celltype_HE_roi1_300dpi.png
D430_RLL_7A2_6_preliminary_celltype_HE_roi1_300dpi.png
 
 
D430_RLL_7A2_6_preliminary_celltype_HE_roi2_300dpi.png
D430_RLL_7A2_6_preliminary_celltype_HE_roi2_300dpi.png
 
 
D430_RLL_7A2_6_preliminary_celltype_HE_whole_300dpi.png
D430_RLL_7A2_6_preliminary_celltype_HE_whole_300dpi.png
 
 
D430_RLL_7A2_6_proseg_qcclass_boundaries_preview.png
D430_RLL_7A2_6_proseg_qcclass_boundaries_preview.png
 
 
D430_RLL_7A2_6_proseg_qcclass_boundaries_whole.png
D430_RLL_7A2_6_proseg_qcclass_boundaries_whole.png
 
 
D430_RLL_7A2_6_proseg_qcclass_qc_panels.pdf
D430_RLL_7A2_6_proseg_qcclass_qc_panels.pdf
 
 
D430_RLL_7A2_6_stardist_qc_center.png
D430_RLL_7A2_6_stardist_qc_center.png
 
 
D430_RLL_7A2_6_stardist_qc_overview.png
D430_RLL_7A2_6_stardist_qc_overview.png
 
 
LungDev_backbone_UMAP_QC_batch_density.png
LungDev_backbone_UMAP_QC_batch_density.png
 
 
Progress_update_20260903.pdf
Progress_update_20260903.pdf
 
 
Sample_D142_RLL_5B1_8_labels_he_expanded_whole.png
Sample_D142_RLL_5B1_8_labels_he_expanded_whole.png
 
 
Sample_D142_RLL_5B1_8_labels_he_whole.png
Sample_D142_RLL_5B1_8_labels_he_whole.png
 
 
Sample_D142_RLL_5B1_8_labels_whole.png
Sample_D142_RLL_5B1_8_labels_whole.png
 
 
Sample_D194_RLL_5A2_6_labels_he_expanded_whole.png
Sample_D194_RLL_5A2_6_labels_he_expanded_whole.png
 
 
Sample_D194_RLL_5A2_6_labels_he_whole.png
Sample_D194_RLL_5A2_6_labels_he_whole.png
 
 
Sample_D194_RLL_5A2_6_labels_whole.png
Sample_D194_RLL_5A2_6_labels_whole.png
 
 
Sample_D327_RLL_4A2_6_labels_he_expanded_whole.png
Sample_D327_RLL_4A2_6_labels_he_expanded_whole.png
 
 
Sample_D327_RLL_4A2_6_labels_he_whole.png
Sample_D327_RLL_4A2_6_labels_he_whole.png
 
 
Sample_D327_RLL_4A2_6_labels_whole.png
Sample_D327_RLL_4A2_6_labels_whole.png
 
 
Sample_D430_RLL_7A2_6_labels_he_expanded_whole.png
Sample_D430_RLL_7A2_6_labels_he_expanded_whole.png
 
 
Sample_D430_RLL_7A2_6_labels_he_whole.png
Sample_D430_RLL_7A2_6_labels_he_whole.png
 
 
Sample_D430_RLL_7A2_6_labels_whole.png
Sample_D430_RLL_7A2_6_labels_whole.png
 
 
all_samples_cell_qc_panels.pdf
all_samples_cell_qc_panels.pdf
 
 
allsamples_2um_eosincon.png
allsamples_2um_eosincon.png
 
 
allsamples_2um_nodepLog1pTotalCounts.png
allsamples_2um_nodepLog1pTotalCounts.png
 
 
barchart_count_celltype_16um.png
barchart_count_celltype_16um.png
 
 
barchart_count_infcelltype_8um.png
barchart_count_infcelltype_8um.png
 
 
barchart_count_qc_D142_RLL_5B1_8_infcelltype_8um.png
barchart_count_qc_D142_RLL_5B1_8_infcelltype_8um.png
 
 
barchart_count_qc_D194_RLL_5A2_6_infcelltype_8um.png
barchart_count_qc_D194_RLL_5A2_6_infcelltype_8um.png
 
 
barchart_count_qc_D327_RLL_4A2_6_infcelltype_8um.png
barchart_count_qc_D327_RLL_4A2_6_infcelltype_8um.png
 
 
barchart_count_qc_D430_RLL_7A2_6_infcelltype_8um.png
barchart_count_qc_D430_RLL_7A2_6_infcelltype_8um.png
 
 
barchart_count_qc_infcelltype_8um.png
barchart_count_qc_infcelltype_8um.png
 
 
barchart_percentage_celltype_16um.png
barchart_percentage_celltype_16um.png
 
 
barchart_percentage_infcelltype_8um.png
barchart_percentage_infcelltype_8um.png
 
 
barchart_percentage_qc_D142_RLL_5B1_8_infcelltype_8um.png
barchart_percentage_qc_D142_RLL_5B1_8_infcelltype_8um.png
 
 
barchart_percentage_qc_D194_RLL_5A2_6_infcelltype_8um.png
barchart_percentage_qc_D194_RLL_5A2_6_infcelltype_8um.png
 
 
barchart_percentage_qc_D327_RLL_4A2_6_infcelltype_8um.png
barchart_percentage_qc_D327_RLL_4A2_6_infcelltype_8um.png
 
 
barchart_percentage_qc_D430_RLL_7A2_6_infcelltype_8um.png
barchart_percentage_qc_D430_RLL_7A2_6_infcelltype_8um.png
 
 
barchart_percentage_qc_infcelltype_8um.png
barchart_percentage_qc_infcelltype_8um.png
 
 
confusionMX_qc_D142_RLL_5B1_8_infcelltype_8um.png
confusionMX_qc_D142_RLL_5B1_8_infcelltype_8um.png
 
 
confusionMX_qc_D194_RLL_5A2_6_infcelltype_8um.png
confusionMX_qc_D194_RLL_5A2_6_infcelltype_8um.png
 
 
confusionMX_qc_D327_RLL_4A2_6_infcelltype_8um.png
confusionMX_qc_D327_RLL_4A2_6_infcelltype_8um.png
 
 
confusionMX_qc_D430_RLL_7A2_6_infcelltype_8um.png
confusionMX_qc_D430_RLL_7A2_6_infcelltype_8um.png
 
 
confusionMX_qc_infcelltype_8um.png
confusionMX_qc_infcelltype_8um.png
 
 
leiden_0p5_canonical_marker_dotplot.png
leiden_0p5_canonical_marker_dotplot.png
 
 
leiden_0p5_lung_program_score_heatmap.png
leiden_0p5_lung_program_score_heatmap.png
 
 
leiden_0p5_preliminary_annotation_UMAP.png
leiden_0p5_preliminary_annotation_UMAP.png
 
 
markergenes_celltypes_16um.png
markergenes_celltypes_16um.png
 
 
markergenes_leiden1.0_16um.png
markergenes_leiden1.0_16um.png
 
 
panel_bins_per_cell.png
panel_bins_per_cell.png
 
 
panel_log10_genes_per_cell.png
panel_log10_genes_per_cell.png
 
 
panel_log10_umis_per_cell.png
panel_log10_umis_per_cell.png
 
 
panel_pct_mito_per_cell.png
panel_pct_mito_per_cell.png
 
 
preview_Sample_D142_RLL_5B1_8_h&e.png
preview_Sample_D142_RLL_5B1_8_h&e.png
 
 
preview_Sample_D194_RLL_5A2_6_h&e.png
preview_Sample_D194_RLL_5A2_6_h&e.png
 
 
preview_Sample_D327_RLL_4A2_6_h&e.png
preview_Sample_D327_RLL_4A2_6_h&e.png
 
 
preview_Sample_D430_RLL_7A2_6_h&e.png
preview_Sample_D430_RLL_7A2_6_h&e.png
 
 
qc_Sample_D142_RLL_5B1_8_m2qcfilter.png
qc_Sample_D142_RLL_5B1_8_m2qcfilter.png
 
 
qc_Sample_D142_RLL_5B1_8_qcclass.png
qc_Sample_D142_RLL_5B1_8_qcclass.png
 
 
qc_Sample_D142_RLL_5B1_8_singlechannel.png
qc_Sample_D142_RLL_5B1_8_singlechannel.png
 
 
qc_Sample_D194_RLL_5A2_6_8.png
qc_Sample_D194_RLL_5A2_6_8.png
 
 

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