Describe the bug
I have a DAPI Image (Channel 3, identifier C3) and a cell Image (Channel 1 or 2, identifier C1 or C2). The sequemtnartion is working well, all 18 cells got identified. But the spot detection table contains only 3 cells.
I do not get any error messages while calculating. In other images it´s working well, but sometimes i have this weird spot detection output.
To Reproduce
I used the identifiers C2 and C3 (DAPI), C1 is analysed separately.
clean segmetnation results or remove cells touching the border did not change anything
select channel: C2
Threshold 200
decompose dense regions: xy=200, z=400
define clusters: min=4, max=300
Logs
Loading plugin FISH-QUANT_mzgca1671722181507 (config=[object Object])
ENGINE_URL=http://XXX.0.0.1:XXX
Connected to an existing server: http://XXX.0.0.1:XXX/
Kernel started: be40d1e0-3556-4e98-9898-1f3347da2a20
Installing requirements for kernel be40d1e0-3556-4e98-9898-1f3347da2a20: ["!python -m pip install big-fish==0.6.2"]
plugin FISH-QUANT (id=FISH-QUANT_mzgca1671722181507) initialized.
Plugin connected.
Setting up plugin.
[FISH-QUANT] plugin initialized.
[FISH-QUANT][scan_folder] received data::
{ "files": [], "file_loaded": "", "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false }
[FISH-QUANT][scan_folder] channel dictionary: {'C2': 'C2', 'C3': 'C3'}
Checking file: /Users/kgDownloads/cell recognition issue/acquisition/C1-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C1', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C3', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C1-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C1', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C2', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C2', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C3', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
[FISH-QUANT][scan_folder] scan results: [{'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif', 'C2': 'C2-slide2_SKBR3_well7_.tif', 'C3': 'C3-slide2_SKBR3_well7_.tif'}, {'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif', 'C2': 'C2-slide2_MCF7_well4_.tif', 'C3': 'C3-slide2_MCF7_well4_.tif'}]
Found 2 images matching the search criteria.
[FISH-QUANT][load_image] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": "", "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "file": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7.tif", "C3": "C3-slide2_SKBR3_well7.tif" }, "create_mips": true, "show_status": true }
[FISH-QUANT][load_image] path for MIPs: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips
[FISH-QUANT][load_image] reading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_mip_dum__C2.png
[FISH-QUANT][load_image] reading image: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_SKBR3_well7_.tif
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_mip_dum__C3.png
[FISH-QUANT][load_image] loaded image: shape: (2, 33, 1040, 1392), dtype: uint16
[FISH-QUANT][filter_image] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "create_mips": true, "show_status": true }
[FISH-QUANT][filter_image] filtering channel C2 with index 0
[ 1, 0.75, 0.75 ]
[FISH-QUANT][filter_image] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_filt_mip_dum_c0.png
[FISH-QUANT][detect_test_thresholds] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][calc_local_max] received data::
{ "minimum_distance": [ 2, 2 ] }
[FISH-QUANT][detect_test_thresholds] testing threshold 0/10: 0.0 yields 409409 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 1/10: 56.0 yields 333110 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 2/10: 111.0 yields 50514 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 3/10: 167.0 yields 4309 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 4/10: 222.0 yields 723 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 5/10: 278.0 yields 259 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 6/10: 333.0 yields 130 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 7/10: 389.0 yields 93 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 8/10: 444.0 yields 66 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 9/10: 500.0 yields 52 spots.
[FISH-QUANT][detect_apply] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][detect_apply] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][detect_apply] detection with threshold 200 detects 1324 spots.
[FISH-QUANT][show_results] received data::
{ "display_type": "dialog", "data_show": [ [ "img_raw", "C2", "mip", "false" ], [ "img_filt", "C2", "mip", "true" ], [ "spots", "3", "true" ] ] }
Adding new layer with specs: ['img_raw', 'C2', 'mip', 'false']
channel_index: 0; image_type: img_raw; display_dim: mip;
Adding new layer with specs: ['img_filt', 'C2', 'mip', 'true']
channel_index: 0; image_type: img_filt; display_dim: mip;
Adding new layer with specs: ['spots', '3', 'true']
[FISH-QUANT][decompose_dense_regions] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][decompose_dense_regions] from 1324 to 2245 spots.
[FISH-QUANT][show_results] received data::
{ "display_type": "dialog", "data_show": [ [ "img_raw", "C2", "mip", "false" ], [ "img_filt", "C2", "mip", "true" ], [ "spots_decompose", "3", "true" ] ] }
Adding nw layer with specs: ['img_raw', 'C2', 'mip', 'false']
channel_index: 0; image_type: img_raw; display_dim: mip;
Adding new layer with specs: ['img_filt', 'C2', 'mip', 'true']
channel_index: 0; image_type: img_filt; display_dim: mip;
Adding new layer with specs: ['spots_decompose', '3', 'true']
[FISH-QUANT][detect_clusters] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true, "name_save": "tmp" }
[FISH-QUANT][detect_clusters] found 56 foci for 2245 spots
[FISH-QUANT][detect_clusters] saving cluster detection results as /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/C2-slide2_SKBR3_well7___cluster_calling.png
[FISH-QUANT][detection_file] received data::
Detection plot present, but removed for display
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false }
[FISH-QUANT][detect_apply] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection" }
[FISH-QUANT][detect_apply] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][detect_apply] save plots with detection results: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection.
[FISH-QUANT][detect_apply] detection with threshold 200 detects 1324 spots.
[FISH-QUANT][save_spots] results (ZYX saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots.csv
[FISH-QUANT][decompose_dense_regions] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection" }
[FISH-QUANT][decompose_dense_regions] from 1324 to 2245 spots.
[FISH-QUANT][detect_clusters] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_foci/C2-slide2_SKBR3_well7___foci_calling" }
[FISH-QUANT][detect_clusters] found 56 foci for 2245 spots
[FISH-QUANT][detect_clusters] saving cluster detection results as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_foci/C2-slide2_SKBR3_well7___foci_calling.png
[FISH-QUANT][save_spots] results (ZYXF saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots_foci.csv
[FISH-QUANT][save_foci] results (<class 'type'> saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___foci.csv
[FISH-QUANT][save_analysis_details]
[FISH-QUANT][save_analysis_details] saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___analysis_details.json
[FISH-QUANT][clean_segmentation] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "C2", "assign_ch_nuc": "C3", "assign_ch_spots": "C2", "remove_cropped_cell": false, "clean_segmentation_enable": true, "plot_individual_cells_enable": false }
Analyzing segmentation result for: /Users/kg/Downloads/cell recognition issue/analysis/segmentation-results/C2-slide2_MCF7_well4___mask__cells.png
Created path to save new segmentation masks: /Users/kg/Downloads/cell recognition issue/analysis/segmentation-results-matched
Analyzing segmentation result for: /Users/kg/Downloads/cell recognition issue/analysis/segmentation-results/C2-slide2_SKBR3_well7___mask__cells.png
[FISH-QUANT][assign_rnas_cells] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "C2", "assign_ch_nuc": "C3", "assign_ch_spots": "C2", "remove_cropped_cell": false, "clean_segmentation_enable": true, "plot_individual_cells_enable": true }
Analyzing spots detection file /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_MCF7_well4___spots.csv
Loading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_MCF7_well4_.tif
Image dimension: 3
Spots (total/cyto/nucleus): 9037/4524/4513
number of cells identified: 1
[ { "cell_id": 10, "bbox": [ 348, 804, 800, 1138 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 104, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 698, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 901, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "uint16", "_rvalue": {} } } ]
Results will be saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/results_per_fov/C2-slide2_MCF7_well4__SPOTS_SUMMARY.csv
Analyzing spots detection file /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots.csv
Loading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
Image dimension: 3
Spots (total/cyto/nucleus): 1324/748/576
number of cells identified: 3
[ { "cell_id": 3, "bbox": [ 0, 830, 320, 1192 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1450, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 790, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 108, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "uint16", "_rvalue": {} } }, { "cell_id": 4, "bbox": [ 14, 524, 320, 818 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1268, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 736, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 65, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "uint16", "_rvalue": {} } }, { "cell_id": 5, "bbox": [ 80, 1126, 400, 1392 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1282, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 370, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 88, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "uint16", "_rvalue": {} } } ]
Results will be saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/results_per_fov/C2-slide2_SKBR3_well7__SPOTS_SUMMARY.csv
Screenshots
ebc-a1ef-95e40b95bdd1.png)
cell_id cell_area nuc_area nb_rna nb_rna_in_nuc nb_rna_out_nuc
3 85112 28424 5550 1913 3637
4 60432 25160 3157 1321 1836
5 58644 4588 5062 470 4592
Versions:
macOS Ventura Version 13.0.1
Chrome Version 108.0.5359.124
Additional context
Thank yout for this software!
The data i used:
https://drive.google.com/drive/folders/1xbkvPNF23Rl7e_d8QSPay4v8s20ozQj8
Describe the bug
I have a DAPI Image (Channel 3, identifier C3) and a cell Image (Channel 1 or 2, identifier C1 or C2). The sequemtnartion is working well, all 18 cells got identified. But the spot detection table contains only 3 cells.
I do not get any error messages while calculating. In other images it´s working well, but sometimes i have this weird spot detection output.
To Reproduce
I used the identifiers C2 and C3 (DAPI), C1 is analysed separately.
clean segmetnation results or remove cells touching the border did not change anything
select channel: C2
Threshold 200
decompose dense regions: xy=200, z=400
define clusters: min=4, max=300
Logs
Loading plugin FISH-QUANT_mzgca1671722181507 (config=[object Object])
ENGINE_URL=http://XXX.0.0.1:XXX
Connected to an existing server: http://XXX.0.0.1:XXX/
Kernel started: be40d1e0-3556-4e98-9898-1f3347da2a20
Installing requirements for kernel be40d1e0-3556-4e98-9898-1f3347da2a20: ["!python -m pip install big-fish==0.6.2"]
plugin FISH-QUANT (id=FISH-QUANT_mzgca1671722181507) initialized.
Plugin connected.
Setting up plugin.
[FISH-QUANT] plugin initialized.
[FISH-QUANT][scan_folder] received data::
{ "files": [], "file_loaded": "", "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false }
[FISH-QUANT][scan_folder] channel dictionary: {'C2': 'C2', 'C3': 'C3'}
Checking file: /Users/kgDownloads/cell recognition issue/acquisition/C1-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C1', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C3', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C1-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C1', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C2', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_MCF7_well4_.tif
... match against regular expression {'channel': 'C2', 'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif'}
Checking file: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_SKBR3_well7_.tif
... match against regular expression {'channel': 'C3', 'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif'}
[FISH-QUANT][scan_folder] scan results: [{'file_ident': 'slide2_SKBR3', 'fov': 'well7', 'img_ext': 'tif', 'C2': 'C2-slide2_SKBR3_well7_.tif', 'C3': 'C3-slide2_SKBR3_well7_.tif'}, {'file_ident': 'slide2_MCF7', 'fov': 'well4', 'img_ext': 'tif', 'C2': 'C2-slide2_MCF7_well4_.tif', 'C3': 'C3-slide2_MCF7_well4_.tif'}]
Found 2 images matching the search criteria.
[FISH-QUANT][load_image] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": "", "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "file": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7.tif", "C3": "C3-slide2_SKBR3_well7.tif" }, "create_mips": true, "show_status": true }
[FISH-QUANT][load_image] path for MIPs: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips
[FISH-QUANT][load_image] reading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_mip_dum__C2.png
[FISH-QUANT][load_image] reading image: /Users/kg/Downloads/cell recognition issue/acquisition/C3-slide2_SKBR3_well7_.tif
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_mip_dum__C3.png
[FISH-QUANT][load_image] loaded image: shape: (2, 33, 1040, 1392), dtype: uint16
[FISH-QUANT][filter_image] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "create_mips": true, "show_status": true }
[FISH-QUANT][filter_image] filtering channel C2 with index 0
[ 1, 0.75, 0.75 ]
[FISH-QUANT][filter_image] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][create_mip] mip saved as: /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/mips/img_filt_mip_dum_c0.png
[FISH-QUANT][detect_test_thresholds] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][calc_local_max] received data::
{ "minimum_distance": [ 2, 2 ] }
[FISH-QUANT][detect_test_thresholds] testing threshold 0/10: 0.0 yields 409409 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 1/10: 56.0 yields 333110 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 2/10: 111.0 yields 50514 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 3/10: 167.0 yields 4309 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 4/10: 222.0 yields 723 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 5/10: 278.0 yields 259 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 6/10: 333.0 yields 130 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 7/10: 389.0 yields 93 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 8/10: 444.0 yields 66 spots.
[FISH-QUANT][detect_test_thresholds] testing threshold 9/10: 500.0 yields 52 spots.
[FISH-QUANT][detect_apply] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][detect_apply] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][detect_apply] detection with threshold 200 detects 1324 spots.
[FISH-QUANT][show_results] received data::
{ "display_type": "dialog", "data_show": [ [ "img_raw", "C2", "mip", "false" ], [ "img_filt", "C2", "mip", "true" ], [ "spots", "3", "true" ] ] }
Adding new layer with specs: ['img_raw', 'C2', 'mip', 'false']
channel_index: 0; image_type: img_raw; display_dim: mip;
Adding new layer with specs: ['img_filt', 'C2', 'mip', 'true']
channel_index: 0; image_type: img_filt; display_dim: mip;
Adding new layer with specs: ['spots', '3', 'true']
[FISH-QUANT][decompose_dense_regions] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true }
[FISH-QUANT][decompose_dense_regions] from 1324 to 2245 spots.
[FISH-QUANT][show_results] received data::
{ "display_type": "dialog", "data_show": [ [ "img_raw", "C2", "mip", "false" ], [ "img_filt", "C2", "mip", "true" ], [ "spots_decompose", "3", "true" ] ] }
Adding nw layer with specs: ['img_raw', 'C2', 'mip', 'false']
channel_index: 0; image_type: img_raw; display_dim: mip;
Adding new layer with specs: ['img_filt', 'C2', 'mip', 'true']
channel_index: 0; image_type: img_filt; display_dim: mip;
Adding new layer with specs: ['spots_decompose', '3', 'true']
[FISH-QUANT][detect_clusters] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "show_status": true, "name_save": "tmp" }
[FISH-QUANT][detect_clusters] found 56 foci for 2245 spots
[FISH-QUANT][detect_clusters] saving cluster detection results as /Users/kg/Downloads/cell recognition issue/analysis/imjoy-tmp/C2-slide2_SKBR3_well7___cluster_calling.png
[FISH-QUANT][detection_file] received data::
Detection plot present, but removed for display
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false }
[FISH-QUANT][detect_apply] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection" }
[FISH-QUANT][detect_apply] name base C2-slide2_SKBR3_well7_
[FISH-QUANT][detect_apply] save plots with detection results: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection.
[FISH-QUANT][detect_apply] detection with threshold 200 detects 1324 spots.
[FISH-QUANT][save_spots] results (ZYX saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots.csv
[FISH-QUANT][decompose_dense_regions] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_detection/C2-slide2_SKBR3_well7___detection" }
[FISH-QUANT][decompose_dense_regions] from 1324 to 2245 spots.
[FISH-QUANT][detect_clusters] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "cy3", "assign_ch_nuc": "dapi", "assign_ch_spots": "cy3", "remove_cropped_cell": false, "clean_segmentation_enable": false, "plot_individual_cells_enable": false, "batch_analysis": false, "create_mips": false, "show_status": false, "analysis_region": [], "name_save": "/Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_foci/C2-slide2_SKBR3_well7___foci_calling" }
[FISH-QUANT][detect_clusters] found 56 foci for 2245 spots
[FISH-QUANT][detect_clusters] saving cluster detection results as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/plots_foci/C2-slide2_SKBR3_well7___foci_calling.png
[FISH-QUANT][save_spots] results (ZYXF saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots_foci.csv
[FISH-QUANT][save_foci] results (<class 'type'> saved as: /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___foci.csv
[FISH-QUANT][save_analysis_details]
[FISH-QUANT][save_analysis_details] saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___analysis_details.json
[FISH-QUANT][clean_segmentation] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results-matched", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "C2", "assign_ch_nuc": "C3", "assign_ch_spots": "C2", "remove_cropped_cell": false, "clean_segmentation_enable": true, "plot_individual_cells_enable": false }
Created path to save new segmentation masks: /Users/kg/Downloads/cell recognition issue/analysis/segmentation-results-matched
[FISH-QUANT][assign_rnas_cells] received data::
{ "files": [ { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, { "file_ident": "slide2_MCF7", "fov": "well4", "img_ext": "tif", "C2": "C2-slide2_MCF7_well4_.tif", "C3": "C3-slide2_MCF7_well4_.tif" } ], "file_loaded": { "file_ident": "slide2_SKBR3", "fov": "well7", "img_ext": "tif", "C2": "C2-slide2_SKBR3_well7_.tif", "C3": "C3-slide2_SKBR3_well7_.tif" }, "path_root": "/Users/kg/Downloads/cell recognition issue", "path_sub_acquisition": "acquisition", "path_sub_analysis": "analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "C2" }, { "name": "C3", "identifier": "C3" } ], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P<file_ident>.)(?P.*).(?P<img_ext>.*)", "current_index": 1, "channel_selected": "C2", "sigma": [ 1, 0.75 ], "threshold_range": [ 0, 500, 10 ], "minimum_distance": [ 2, 2 ], "detection_threshold": 200, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": true, "create_plots": true, "show_filtered": true, "show_detection": true, "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "assign_subfolder": "segmentation-results", "assign_subfolder_new": "segmentation-results", "assign_ident_spots": "__spots.csv", "assign_ident_cell": "__mask__cells.png", "assign_ident_nuc": "__mask__nuclei.png", "assign_ch_cell": "C2", "assign_ch_nuc": "C3", "assign_ch_spots": "C2", "remove_cropped_cell": false, "clean_segmentation_enable": true, "plot_individual_cells_enable": true }
Analyzing spots detection file /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_MCF7_well4___spots.csv
Loading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_MCF7_well4_.tif
Image dimension: 3
Spots (total/cyto/nucleus): 9037/4524/4513
number of cells identified: 1
[ { "cell_id": 10, "bbox": [ 348, 804, 800, 1138 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 104, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 698, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 901, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 452, 334 ], "_rdtype": "uint16", "_rvalue": {} } } ]
Results will be saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/results_per_fov/C2-slide2_MCF7_well4__SPOTS_SUMMARY.csv
Analyzing spots detection file /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/C2-slide2_SKBR3_well7___spots.csv
Loading image: /Users/kg/Downloads/cell recognition issue/acquisition/C2-slide2_SKBR3_well7_.tif
Image dimension: 3
Spots (total/cyto/nucleus): 1324/748/576
number of cells identified: 3
[ { "cell_id": 3, "bbox": [ 0, 830, 320, 1192 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1450, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 790, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 108, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 320, 362 ], "_rdtype": "uint16", "_rvalue": {} } }, { "cell_id": 4, "bbox": [ 14, 524, 320, 818 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1268, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 736, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 65, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 306, 294 ], "_rdtype": "uint16", "_rvalue": {} } }, { "cell_id": 5, "bbox": [ 80, 1126, 400, 1392 ], "cell_coord": { "_rtype": "ndarray", "_rshape": [ 1282, 2 ], "_rdtype": "int64", "_rvalue": {} }, "cell_mask": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "bool", "_rvalue": {} }, "nuc_coord": { "_rtype": "ndarray", "_rshape": [ 370, 2 ], "_rdtype": "int64", "_rvalue": {} }, "nuc_mask": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "bool", "_rvalue": {} }, "rna_coord": { "_rtype": "ndarray", "_rshape": [ 88, 3 ], "_rdtype": "int64", "_rvalue": {} }, "image": { "_rtype": "ndarray", "_rshape": [ 320, 266 ], "_rdtype": "uint16", "_rvalue": {} } } ]
Results will be saved as /Users/kg/Downloads/cell recognition issue/analysis/spot_detection/results_per_fov/C2-slide2_SKBR3_well7__SPOTS_SUMMARY.csv
Screenshots
ebc-a1ef-95e40b95bdd1.png)
cell_id cell_area nuc_area nb_rna nb_rna_in_nuc nb_rna_out_nuc
3 85112 28424 5550 1913 3637
4 60432 25160 3157 1321 1836
5 58644 4588 5062 470 4592
Versions:
macOS Ventura Version 13.0.1
Chrome Version 108.0.5359.124
Additional context
Thank yout for this software!
The data i used:
https://drive.google.com/drive/folders/1xbkvPNF23Rl7e_d8QSPay4v8s20ozQj8