Files used in this project
Segmentation:
Mesmer: KK003_1_Segment_Image_Data.ipynb
Cellpose: cell_segmentation_Cellpose.ipynb & KK003_cell_table_export_CellPose.ipynb
Clustering:
Mesmer/Scyan: KK_BC25_21_1_MesmerScyanv2_KK003.ipynb
Cellpose/Scyan: KK_BC25_21_1_CellposeScyanv2_KK003.ipynb
Mesmer/Pixie: KK003_2_Pixie_Cluster_Pixels.ipynb & KK003_3_Pixie_Cluster_Cells.ipynb
Downstream analysis using Mesmer/Scyan:
Scanpy and Seaborn: KK_BC25_21_1_Analysis_Mesmerscyanv2_KK003.ipynb
Squidpy (tried but not included in report): KK_BC25_21_1_analysis_squidpy_KK003.ipynb