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github.com/CellProfiler/CellProfiler-plugins
/ functions
Functions
1,666 in github.com/CellProfiler/CellProfiler-plugins
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Functions
1,666
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Types & classes
129
Method
__init__
(self, gt_snake, grown_snake, avg_cell_diameter, params)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py:19
Method
__init__
(self, size=None, xmax=1, xmin=0)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py:29
Method
__init__
(self, seed, image_repo, params, best_snake=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:24
Method
__init__
(self, binary_mask, seed=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:123
Method
__init__
(self, target, callback, *args)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:1112
Method
__init__
:param server_url: Server URL for MONAILabel (e.g. http://127.0.0.1:8000) :param tmpdir: Temp directory to save temporary files. If
active_plugins/runvista2d.py:74
Method
__init__
:param error: Error code represented by MONAILabelError :param msg: Error message :param status_code: HTTP Response code
active_plugins/runvista2d.py:516
Method
__init__
(self)
active_plugins/runimagejscript.py:137
Method
__init__
(self, text, value, *args, **kwargs)
active_plugins/cpij/server.py:82
Method
__repr__
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/point.py:25
Function
_start_server
Start the server that will be used for sending communication between ImageJ and CellProfiler. NB: this method will permanently block its
active_plugins/cpij/server.py:409
Function
add_mutations
(gt_and_grown, avg_cell_diameter)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py:17
Function
add_snake
(snakes, snake)
unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py:87
Method
analyzeDistances
(PSD_polar, frequencies_polar)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:937
Method
analyzeDistances
(PSD_polar, frequencies_polar)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:937
Method
analyzeOrientations
(PSD_polar, rotate90=True)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:817
Method
analyzeOrientations
(PSD_polar, rotate90=True)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:816
Method
auth_enabled
Check if Auth is enabled
active_plugins/runvista2d.py:113
Method
auth_token
Fetch Auth Token. Currently only basic authentication is supported. :param username: UserName for basic authentication :par
active_plugins/runvista2d.py:128
Method
auth_valid_token
(self)
active_plugins/runvista2d.py:149
Method
background
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:20
Method
background_mask
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:80
Method
brighter
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:31
Method
brighter_original
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:38
Function
calc_ranking
(rank_snakes, pf_param_vector)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:106
Method
calculate_area_multiplier
(area)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:740
Method
calculate_area_multiplier
(area)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:743
Method
call_by_column
(base_array)
active_plugins/callbarcodes.py:675
Method
cell_border_mask
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:94
Method
cell_content_mask
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:87
Method
centroid
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:37
Method
checkShapesEqual
(w, alpha)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:422
Method
checkShapesEqual
(w, alpha)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:420
Method
circ_confmean
Computes the confidence limits on the mean for circular data. Input: alpha sample of angles
unmaintained_plugins/CellProfiler3/spectralanalysis.py:473
Method
circ_confmean
Computes the confidence limits on the mean for circular data. Input: alpha sample of angles
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:471
Method
circ_dist
Pairwise difference x_i-y_i around the circle computed efficiently. Input: x sample of
unmaintained_plugins/CellProfiler3/spectralanalysis.py:696
Method
circ_dist
Pairwise difference x_i-y_i around the circle computed efficiently. Input: x sample of
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:695
Method
circ_kurtosis
(alpha, w, dim=0)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:773
Method
circ_kurtosis
(alpha, w, dim=0)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:772
Method
circ_mean
Computes the mean direction for circular data. Input: alpha sample of angles in radians
unmaintained_plugins/CellProfiler3/spectralanalysis.py:529
Method
circ_mean
Computes the mean direction for circular data. Input: alpha sample of angles in radians
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:528
Method
circ_moment
Calculates the complex p-th centred or non-centred moment of the angular data in angle. Input
unmaintained_plugins/CellProfiler3/spectralanalysis.py:650
Method
circ_moment
Calculates the complex p-th centred or non-centred moment of the angular data in angle. Input
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:649
Method
circ_r
Computes mean resultant vector length for circular data. Input: alpha sample of angles in radi
unmaintained_plugins/CellProfiler3/spectralanalysis.py:430
Method
circ_r
Computes mean resultant vector length for circular data. Input: alpha sample of angles in radi
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:428
Method
circ_rad2ang
(alpha)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:813
Method
circ_rad2ang
(alpha)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:812
Method
circ_skewness
(alpha, w, dim=0)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:733
Method
circ_skewness
(alpha, w, dim=0)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:732
Method
circ_std
Computes circular standard deviation for circular data (equ. 26.20, Zar). Input:
unmaintained_plugins/CellProfiler3/spectralanalysis.py:609
Method
circ_std
Computes circular standard deviation for circular data (equ. 26.20, Zar). Input:
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:608
Method
circ_var
Computes circular variance for circular data (equ. 26.17/18, Zar). Input:
unmaintained_plugins/CellProfiler3/spectralanalysis.py:565
Method
circ_var
Computes circular variance for circular data (equ. 26.17/18, Zar). Input:
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:564
Method
compute_median_abs_deviation
(values_lists)
unmaintained_plugins/CellProfiler3/measuretrackquality.py:549
Method
compute_median_abs_deviation
(values_lists)
unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py:551
Method
compute_single_aberration
Figure out the deviation from smooth at each time point :param normalized_values: time series of values, normalized to the ty
unmaintained_plugins/CellProfiler3/measuretrackquality.py:398
Method
compute_single_aberration
Figure out the deviation from smooth at each time point :param normalized_values: time series of values, normalized to the ty
unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py:400
Function
contact_area_params
(request)
unmaintained_tests/test_mergeobjects.py:73
Function
convert_java_type_to_setting
Helper method to convert ImageJ/Java class parameter types to CellProfiler settings Parameters ---------- param_name : str, required
active_plugins/cpij/server.py:211
Function
convert_outlines_to_objects
(outlines, diameter)
unmaintained_plugins/CellProfiler3/convertoutlinestoobjects.py:68
Function
convert_outlines_to_objects
(outlines, diameter)
active_plugins/convertoutlinestoobjects.py:68
Method
create_data_for_measurement
(target_median)
unmaintained_tests/test_measuretrackquality.py:42
Function
create_mutation
(org_snake, polar_transform, dilation)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py:74
Function
create_poly_mutation
(org_snake, polar_transform, max_diff)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py:53
Method
create_session
Create New Session :param image_in: filepath for image to be sent to server as part of session creation :param params: addit
active_plugins/runvista2d.py:193
Method
create_settings
(self)
unmaintained_plugins/CellProfiler4/declumpobjects.py:57
Method
create_settings
Create the settings for the module at startup. The module allows for an unlimited number of measured objects, each of which h
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:180
Method
create_settings
Create the settings for the module at startup.
unmaintained_plugins/CellProfiler2/calculatehistogram.py:51
Method
create_settings
(self)
unmaintained_plugins/CellProfiler2/transform.py:107
Method
create_settings
Create the settings for the module at startup.
unmaintained_plugins/CellProfiler2/calculatemoments.py:111
Method
create_settings
Create the settings for the module Create the settings for the module during initialization.
unmaintained_plugins/CellProfiler2/identifylinearobjects.py:38
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/DoGNet.py:54
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/predict.py:72
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/nucleaizer.py:65
Method
create_settings
Create the settings for the module at startup. The module allows for an unlimited number of measured objects, each of which h
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:179
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/randomwalkeralgorithm.py:26
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/imagegradient.py:25
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/seedobjects.py:56
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/measureimagefocus.py:35
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:212
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:33
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/save_16bit_pngs.py:104
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:52
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/measure_population_context.py:59
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/blobdetection.py:39
Method
create_settings
Create the settings for the module at startup.
unmaintained_plugins/CellProfiler3/calculatehistogram.py:51
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/measuretrackquality.py:111
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/convertoutlinestoobjects.py:35
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/shollanalysis.py:142
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/measureradialentropy.py:28
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/edgedetection.py:26
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/transform.py:107
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/laplacianofgaussian.py:19
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/thresh_all.py:106
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/rescale_mean_sd.py:104
Method
create_settings
Create the settings for the ExportToCellH5 module
unmaintained_plugins/CellProfiler3/exporttocellh5.py:65
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/compensatecolors.py:94
Method
create_settings
Create the settings for the module at startup.
unmaintained_plugins/CellProfiler3/calculatemoments.py:111
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/tophattransform.py:24
Method
create_settings
(self)
unmaintained_plugins/CellProfiler3/runimagej.py:77
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