spotmax 1.0.3__py3-none-any.whl

examples/ini_config_files_templates/example_config_params_mitochondria.ini

@@ -0,0 +1,92 @@
+[File paths and channels]
+Experiment folder path(s) to analyse = 
+	.\data\test_multi_pos_analyse_single_pos
+Spots channel end name = mNeon
+Cells segmentation end name = segm.npz
+Reference channel end name = mKate
+Spots channel segmentation end name = 
+Ref. channel segmentation end name = 
+Table with lineage info end name = 
+Run number = 1
+Text to append at the end of the output files = 
+File extension of the output tables = .h5
+Spots coordinates table end name = 
+
+[METADATA]
+Number of frames (SizeT) = 1
+Analyse until frame number = 1
+Number of z-slices (SizeZ) = 43
+Pixel width (μm) = 0.0603516
+Pixel height (μm) = 0.0602969
+Voxel depth (μm) = 0.2857143
+Numerical aperture = 1.4
+Spots reporter emission wavelength (nm) = 500.0
+Spot minimum z-size (μm) = 1.0
+Resolution multiplier in y- and x- direction = 1.0
+Spot (z, y, x) minimum dimensions (radius) = (3.5, 3.61, 3.61) pixel
+	(1.0, 0.218, 0.218) micrometer
+
+[Pre-processing]
+Aggregate cells prior analysis = False
+Remove hot pixels = False
+Initial gaussian filter sigma = 0.75
+Sharpen spots signal prior detection = True
+Extend 3D input segm. objects in Z = (0, 0)
+
+[Reference channel]
+Segment reference channel = True
+Keep only spots that are inside ref. channel mask = True
+Use the ref. channel mask to determine background = True
+Ref. channel is single object (e.g., nucleus) = False
+Ref. channel gaussian filter sigma = 0.75
+Sigmas used to enhance network-like structures = [1.0, 2.0]
+Ref. channel segmentation method = Thresholding
+Ref. channel threshold function = threshold_yen
+Features for filtering ref. channel objects = 
+	sub_obj_vol_vox, 10, None
+Save reference channel features = True
+Save reference channel segmentation masks = True
+Save pre-processed reference channel image = True
+
+[Spots channel]
+Spots segmentation method = Thresholding
+Spot detection threshold function = threshold_yen
+Spots detection method = peak_local_max
+Features and thresholds for filtering true spots = 
+	spot_vs_ref_ch_ttest_pvalue, None, 0.025
+	spot_vs_ref_ch_ttest_tstat, 0.0, None
+Optimise detection for high spot density = True
+Compute spots size (fit gaussian peak(s)) = True
+After spotFIT, drop spots that are too close = True
+Save spots segmentation masks = True
+Save pre-processed spots image = True
+Minimum size of spot segmentation mask = 5
+
+[SpotFIT]
+Bounds interval for the x and y peak center coord. = 0.1
+Bounds interval for the z peak center coord. = 0.2
+Bounds for sigma in x-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in y-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in z-direction = 0.5, spotsize_z_radius_pxl
+Bounds for the peak amplitude = 0.0, spotsize_A_max
+Bounds for the peak background level = spot_B_min, inf
+Initial guess for sigma in x-direction = spotsize_initial_radius_yx_pixel
+Initial guess for sigma in y-direction = spotsize_initial_radius_yx_pixel
+Initial guess for sigma in z-direction = spotsize_initial_radius_z_pixel
+Initial guess for the peak amplitude = spotsize_A_max
+Initial guess for the peak background level = spotsize_surface_median
+
+[Custom combined measurements]
+Column name = 
+
+[Configuration]
+Folder path of the log file = ~\spotmax_appdata\logs
+Folder path of the final report = .\data\test_multi_pos_analyse_single_pos
+Filename of final report = 2024-03-12_09-00-34_example_config_params_mitochondria_spotMAX_report.rst
+Disable saving of the final report = False
+Use default values for missing parameters = False
+Stop analysis on critical error = True
+Use CUDA-compatible GPU = False
+Number of threads used by numba = 2
+Reduce logging verbosity = False
+

examples/ini_config_files_templates/example_config_params_smFISH.ini

@@ -0,0 +1,60 @@
+[File paths and channels]
+Experiment folder path(s) to analyse = 
+	.\data\test_multi_pos_analyse_single_pos\Position_16\
+Spots channel end name = mNeon
+Cells segmentation end name = segm
+Reference channel end name = DAPI
+Ref. channel segmentation end name = 
+Table with lineage info end name = 
+Run number = 11
+Text to append at the end of the output files = descriptive_name
+File extension of the output tables = .csv
+
+[METADATA]
+Number of frames (SizeT) = 1
+Analyse until frame number = 1
+Number of z-slices (SizeZ) = 43
+Pixel width (μm) = 0.06725
+Pixel height (μm) = 0.06725
+Voxel depth (μm) = 0.35
+Numerical aperture = 1.4
+Spots reporter emission wavelength (nm) = 509.0
+Spot minimum z-size (μm) = 1.0
+Resolution multiplier in y- and x- direction = 1.0
+
+[Pre-processing]
+Aggregate cells prior analysis = True
+Initial gaussian filter sigma = 0.75
+Sharpen spots signal prior detection = True
+Remove hot pixels = False
+
+[Reference channel]
+Segment reference channel = False
+Keep only spots that are inside ref. channel mask = False
+Use the ref. channel mask to determine background = False
+Ref. channel is single object (e.g., nucleus) = True
+Ref. channel threshold function = threshold_li
+Calculate reference channel network length = False
+Save reference channel segmentation masks = True
+
+[Spots channel]
+Spots detection method = peak_local_max
+Spots segmentation method = Thresholding
+Spot detection threshold function = threshold_li
+Features and thresholds for filtering true spots = 
+	spot_vs_backgr_effect_size_glass, 0.8, None
+Compute spots size = True
+Optimise detection for high spot density = True
+Save spots segmentation masks = False
+
+[Configuration]
+Folder path of the final report = .\data\test_multi_pos_analyse_single_pos\Position_16\
+Disable saving of the final report = False
+Use default values for missing parameters = True
+Stop analysis on critical error = True
+Number of threads used by numba = 2
+Filename of final report = 2023-08-04_20-55-50_example_config_params_smFISH_spotMAX_report.rst
+Folder path of the log file = ~\spotmax_appdata\logs
+Use CUDA-compatible GPU = False
+Reduce logging verbosity = False
+

examples/ini_config_files_templates/mtDNA_yeast_tutorial_parameters.ini

@@ -0,0 +1,112 @@
+[File paths and channels]
+Experiment folder path(s) to analyse = spotmax\docs\source\tutorials\data\mtDNA_mito_yeast\Position_26
+Spots channel end name = mNeon
+Cells segmentation end name = segm.npz
+Reference channel end name = mKate
+Spots channel segmentation end name = 
+Ref. channel segmentation end name = 
+Table with lineage info end name = acdc_output
+Run number = 1
+Text to append at the end of the output files = tutorial
+File extension of the output tables = .h5
+Spots coordinates table end name = 
+
+[METADATA]
+Number of frames (SizeT) = 1
+Analyse until frame number = 1
+Number of z-slices (SizeZ) = 43
+Pixel width (μm) = 0.0672498
+Pixel height (μm) = 0.0672498
+Voxel depth (μm) = 0.35
+Numerical aperture = 1.4
+Spots reporter emission wavelength (nm) = 500.0
+Spot minimum z-size (μm) = 1.0
+Resolution multiplier in y- and x- direction = 2.0
+Spot (z, y, x) minimum dimensions (radius) = (2.86, 6.48, 6.48) pixel
+	(1.0, 0.436, 0.436) micrometer
+
+[Pre-processing]
+Aggregate cells prior analysis = False
+Remove hot pixels = False
+Initial gaussian filter sigma = 0.75
+Sharpen spots signal prior detection = True
+Extend 3D input segm. objects in Z = (0, 0)
+
+[Reference channel]
+Segment reference channel = True
+Keep only spots that are inside ref. channel mask = False
+Use the ref. channel mask to determine background = True
+Ref. channel is single object (e.g., nucleus) = False
+Ref. channel gaussian filter sigma = 0.75
+Sigmas used to enhance network-like structures = [2.0, 3.0]
+Ref. channel segmentation method = Thresholding
+Ref. channel threshold function = threshold_yen
+Save reference channel segmentation masks = False
+Save pre-processed reference channel image = False
+Features for filtering ref. channel objects = 
+Save reference channel features = False
+Keep external touching objects intact = False
+
+[Spots channel]
+Spots segmentation method = spotMAX AI
+Spot detection threshold function = threshold_li
+Spots detection method = peak_local_max
+Features and thresholds for filtering true spots = 
+	spot_vs_backgr_ttest_pvalue, None, 0.025
+	spot_vs_ref_ch_ttest_tstat, 0.0, None
+Optimise detection for high spot density = True
+Compute spots size (fit gaussian peak(s)) = False
+Save spots segmentation masks = True
+Save pre-processed spots image = False
+Minimum size of spot segmentation mask = 5
+Local background ring width = 0.336249 micrometre
+After spotFIT, drop spots that are too close = False
+Merge spots pairs where single peak fits better = False
+Maximum number of spot pairs to check = 11
+Skip objects where segmentation failed = False
+
+[SpotFIT]
+Bounds interval for the x and y peak center coord. = 0.1
+Bounds interval for the z peak center coord. = 0.2
+Bounds for sigma in x-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in y-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in z-direction = 0.5, spotsize_z_radius_pxl
+Bounds for the peak amplitude = 0.0, spotsize_A_max
+Bounds for the peak background level = spot_B_min, inf
+Initial guess for sigma in x-direction = x_resolution_pxl/2.35
+Initial guess for sigma in y-direction = y_resolution_pxl/2.35
+Initial guess for sigma in z-direction = z_resolution_pxl/2.35
+Initial guess for the peak amplitude = spotsize_A_max
+Initial guess for the peak background level = spotsize_surface_median
+
+[Configuration]
+Folder path of the log file = ~\spotmax_appdata\logs
+Folder path of the final report = 
+Filename of final report = do_not_save
+Disable saving of the final report = True
+Use default values for missing parameters = False
+Stop analysis on critical error = True
+Use CUDA-compatible GPU = False
+Number of threads used by numba = 4
+Reduce logging verbosity = False
+
+[neural_network.init.spots]
+model_type = 2D
+preprocess_across_experiment = False
+preprocess_across_timepoints = False
+gaussian_filter_sigma = 0.0
+remove_hot_pixels = False
+config_yaml_filepath = spotmax\nnet\config.yaml
+PhysicalSizeX = 0.0672498
+resolution_multiplier_yx = 1.0
+use_gpu = False
+save_prediction_map = False
+verbose = True
+
+[neural_network.segment.spots]
+threshold_value = 0.9
+label_components = False
+
+[Custom combined measurements]
+Column name = 
+

examples/ini_config_files_templates/smFISH_yeast_tutorial_parameters.ini

@@ -0,0 +1,89 @@
+[File paths and channels]
+Experiment folder path(s) to analyse = /spotmax/docs/source/tutorials/data/smFISH_yeast/Position_2
+Spots channel end name = MDN1
+Cells segmentation end name = segm.npz
+Reference channel end name = DAPI
+Spots channel segmentation end name = 
+Ref. channel segmentation end name = 
+Table with lineage info end name = acdc_output.csv
+Run number = 1
+Text to append at the end of the output files = tutorial
+File extension of the output tables = .csv
+
+[METADATA]
+Number of frames (SizeT) = 1
+Analyse until frame number = 1
+Number of z-slices (SizeZ) = 25
+Pixel width (μm) = 0.07206
+Pixel height (μm) = 0.07206
+Voxel depth (μm) = 0.24
+Numerical aperture = 1.4
+Spots reporter emission wavelength (nm) = 668.0
+Spot minimum z-size (μm) = 1.0
+Resolution multiplier in y- and x- direction = 1.5
+Spot (z, y, x) minimum dimensions (radius) = (4.17, 6.06, 6.06) pixel
+                                             (1.0, 0.437, 0.437) micrometer
+
+[Pre-processing]
+Aggregate cells prior analysis = True
+Remove hot pixels = False
+Initial gaussian filter sigma = 0.75
+Sharpen spots signal prior detection = True
+
+[Reference channel]
+Segment reference channel = True
+Keep only spots that are inside ref. channel mask = False
+Use the ref. channel mask to determine background = False
+Ref. channel is single object (e.g., nucleus) = True
+Ref. channel gaussian filter sigma = 2.0
+Sigmas used to enhance network-like structures = 0.0
+Ref. channel segmentation method = Thresholding
+Ref. channel threshold function = threshold_otsu
+Save reference channel segmentation masks = False
+Save pre-processed reference channel image = False
+
+[Spots channel]
+Spots segmentation method = spotMAX AI
+Spot detection threshold function = threshold_li
+Spots detection method = peak_local_max
+Features and thresholds for filtering true spots = 
+Optimise detection for high spot density = True
+Compute spots size (fit gaussian peak(s)) = False
+Save spots segmentation masks = False
+Save pre-processed spots image = False
+
+[SpotFIT]
+Bounds interval for the x and y peak center coord. = 0.1
+Bounds interval for the z peak center coord. = 0.2
+Bounds for sigma in x-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in y-direction = 0.5, spotsize_yx_radius_pxl
+Bounds for sigma in z-direction = 0.5, spotsize_z_radius_pxl
+Bounds for the peak amplitude = 0.0, spotsize_A_max
+Bounds for the peak background level = spot_B_min, inf
+
+[Configuration]
+Folder path of the log file = ~\spotmax_appdata\logs
+Folder path of the final report = 
+Filename of final report = 
+Disable saving of the final report = False
+Use default values for missing parameters = False
+Stop analysis on critical error = True
+Use CUDA-compatible GPU = False
+Number of threads used by numba = -1
+Reduce logging verbosity = False
+
+[neural_network.init.spots]
+model_type = 2D
+preprocess_across_experiment = False
+preprocess_across_timepoints = False
+gaussian_filter_sigma = 1.0
+remove_hot_pixels = False
+config_yaml_filepath = /spotmax/nnet/config.yaml
+PhysicalSizeX = 0.07206
+resolution_multiplier_yx = 1.0
+use_gpu = False
+
+[neural_network.segment.spots]
+threshold_value = 0.9
+label_components = False
+