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Functions1,666 in github.com/CellProfiler/CellProfiler-plugins

⨍ Functions 1,666◇ Types & classes 129
↓ 1 callersFunctionhaar_synthesis
(image)
unmaintained_plugins/CellProfiler3/transformfilters.py:342
↓ 1 callersFunctionhaar_synthesis
(image)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:342
↓ 1 callersFunctionhack_add_from_file_into_EditObjects
(dialog_box)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:166
↓ 1 callersFunctionhack_add_from_file_into_EditObjects
(dialog_box)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:169
↓ 1 callersMethodhttp_upload
(method, server_url, selector, fields, files, headers=None)
active_plugins/runvista2d.py:561
↓ 1 callersFunctionimage_blur
Performs image blur with kernel: [[2, 3, 2], [3, 12, 3], [2, 3, 2]] / 32 @param image: image to be blurred (assumed as numpy.array of values
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:241
↓ 1 callersFunctionimage_dilate_with_element
(image, n)
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:95
↓ 1 callersMethodinfer
Run Infer :param model: Name of Model :param image_id: Image Id :param params: Additional configs/json params as par
active_plugins/runvista2d.py:352
↓ 1 callersMethodinference
(self, net,image,get_intermediate=False)
unmaintained_plugins/CellProfiler3/DoGNet.py:167
↓ 1 callersMethodinference
(self, net,image,get_intermediate=False)
unmaintained_plugins/CellProfiler4_autoconverted/DoGNet.py:168
↓ 1 callersMethodinit_filter
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:88
↓ 1 callersMethodinit_seeder
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:85
↓ 1 callersMethodinit_segmentation
(self)
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:157
↓ 1 callersMethodinside
(self, x, y)
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:319
↓ 1 callersFunctioninverse_simoncelli_transform_pyramid
(image, scale, mask=None)
unmaintained_plugins/CellProfiler3/transformfilters.py:117
↓ 1 callersFunctioninverse_simoncelli_transform_pyramid
(image, scale, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:117
↓ 1 callersFunctioninverse_simoncelli_transform_redundant
(image, scale, mask=None)
unmaintained_plugins/CellProfiler3/transformfilters.py:215
↓ 1 callersFunctioninverse_simoncelli_transform_redundant
(image, scale, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:215
↓ 1 callersMethodis_alive
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:1141
↓ 1 callersMethodis_alive
(self)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:1144
↓ 1 callersMethodis_inside
Check if seed is inside of eroded mask. @type seed: Seed
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:140
↓ 1 callersFunctionis_server_running
Helper method to determine if the ImageJ server is up and running. Parameters ---------- timeout : number, optional (default 0.25)
active_plugins/cpij/server.py:441
↓ 1 callersMethodis_single_snake_discarded
@type snake: Snake @rtype: bool
unmaintained_plugins/CellProfiler3/cellstar/core/snake_filter.py:30
↓ 1 callersFunctionkeep_3_best
(partial_parameters, distance)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:79
↓ 1 callersMethodkeep_by_string
workspace - workspace passed into Run src_objects - the Objects instance to be filtered
active_plugins/filterobjects_stringmatch.py:227
↓ 1 callersFunctionlock
Helper method to synchronzie requests with the ImageJ server. A lock should be acquired before sending data to the server, and released afte
active_plugins/cpij/bridge.py:34
↓ 1 callersFunctionlog_ndi
unmaintained_plugins/CellProfiler3/compensatecolors.py:543
↓ 1 callersMethodlog_ndi
active_plugins/compensatecolors.py:560
↓ 1 callersFunctionloop_connected_components
@type mask: np.ndarray @rtype (np.ndarray, np.ndarray, np.ndarray)
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:50
↓ 1 callersFunctionmain
Start the two pyimagej server components: - This will create a new "imagej-server" thread that handles inter-process communication
active_plugins/cpij/server.py:485
↓ 1 callersMethodmake_workspace
Make a workspace for running Threshold. Taken from CellProfiler's test suite.
unmaintained_plugins/CellProfiler3/thresh_all.py:567
↓ 1 callersMethodmake_workspace
Make a workspace for running Threshold. Taken from CellProfiler's test suite.
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:577
↓ 1 callersFunctionmask_with_pil
(ys, xs, yslice, xslice)
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:183
↓ 1 callersFunctionmaximal_distance
(n)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:59
↓ 1 callersMethodmeasure
(self, image, workspace)
unmaintained_plugins/CellProfiler3/shollanalysis.py:294
↓ 1 callersMethodmeasure
(self, image, workspace)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:297
↓ 1 callersFunctionmerge_objects
(labels, diameter, planewise, remove_below_threshold, use_contact_area, contact_area_method,
unmaintained_plugins/CellProfiler3/mergeobjects.py:245
↓ 1 callersFunctionmerge_objects
(labels, diameter, planewise, remove_below_threshold, use_contact_area, contact_area_method,
unmaintained_plugins/CellProfiler4_autoconverted/mergeobjects.py:248
↓ 1 callersMethodmerge_parameters_with_me
(self, new_params)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:54
↓ 1 callersMethodmergeduplicates
(self, firstlabel,secondlabel,labeldict,angledict)
unmaintained_plugins/CellProfiler2/identifylinearobjects.py:361
↓ 1 callersMethodmergeduplicates
(self, firstlabel,secondlabel,labeldict,angledict)
unmaintained_plugins/CellProfiler3/identifylinearobjects.py:361
↓ 1 callersMethodmergeduplicates
(self, firstlabel,secondlabel,labeldict,angledict)
unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py:363
↓ 1 callersMethodmulti_fitness
(self, gt_snake)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:118
↓ 1 callersFunctionmultiproc_optimize
(images, gt_snakes, method='brute', initial_params=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:325
↓ 1 callersMethodnormalized_log
Perform the Laplacian of Gaussian transform on the image image - 2-d image array mask - binary mask of significant pixels si
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:759
↓ 1 callersMethodnormalized_log
Perform the Laplacian of Gaussian transform on the image image - 2-d image array mask - binary mask of significant pixels si
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:762
↓ 1 callersFunctionoptimize
(method_name, encoded_params, distance_function)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:260
↓ 1 callersFunctionoptimize
(method_name, gt_snakes, images, params, precision, avg_cell_diameter)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:227
↓ 1 callersFunctionoptimize_basinhopping
(params_to_optimize, distance_function)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:300
↓ 1 callersMethodout_of_gt_penalty
(snake_area, gt_snake_area, intersection)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:101
↓ 1 callersFunctionparameters_from_segmentation_precision
(parameters, segmentation_precision)
unmaintained_plugins/CellProfiler3/cellstar/utils/params_util.py:43
↓ 1 callersMethodparse_multipart
(fp, headers)
active_plugins/runvista2d.py:674
↓ 1 callersFunctionpf_get_distances
(gt_snakes, images, initial_parameters, callback=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:154
↓ 1 callersFunctionpf_rank_get_ranking
(rank_snakes, initial_parameters)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:121
↓ 1 callersFunctionpf_rank_parameters_encode
avgBorderBrightnessWeight: 300 avgInnerBrightnessWeight: 10 avgInnerDarknessWeight: 0 logAreaBonus: 18 maxInnerBrightnessWeight:
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py:112
↓ 1 callersFunctionpolynomial
(x1, x2)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_mutator.py:58
↓ 1 callersMethodpre_process
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:155
↓ 1 callersFunctionprepare_snake_seed_pairs
(gt_snakes, initial_parameters)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:143
↓ 1 callersMethodqueryall
(self,barcodeset, query)
unmaintained_plugins/CellProfiler3/callbarcodes.py:509
↓ 1 callersMethodqueryall
(self, cropped_barcode_dict, query)
active_plugins/callbarcodes.py:797
↓ 1 callersMethodranking_parameters_vector
(self, ranking_params)
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:360
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler2/calculatehistogram.py:388
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler2/calculatemoments.py:382
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler3/calculatehistogram.py:388
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler3/calculatemoments.py:382
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:389
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:388
↓ 1 callersMethodrecord_image_measurement
Record the result of a measurement in the workspace's measurements
active_plugins/calculatemoments.py:430
↓ 1 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler2/calculatemoments.py:365
↓ 1 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler3/calculatemoments.py:365
↓ 1 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:370
↓ 1 callersMethodrecord_measurement
Record the result of a measurement in the workspace's measurements
active_plugins/calculatemoments.py:414
↓ 1 callersFunctionrun
(image, gt_snakes, precision, avg_cell_diameter, method='brute', initial_params=None, background_image=None,
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:191
↓ 1 callersMethodrun
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:1122
↓ 1 callersMethodrun
(self)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:1125
↓ 1 callersMethodrun_global_otsu_2
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:611
↓ 1 callersMethodrun_global_otsu_2
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:620
↓ 1 callersMethodrun_global_otsu_3b
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:626
↓ 1 callersMethodrun_global_otsu_3b
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:635
↓ 1 callersMethodrun_global_otsu_3f
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:618
↓ 1 callersMethodrun_global_otsu_3f
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:627
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:785
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler2/calculatehistogram.py:214
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler2/calculatemoments.py:243
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:784
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler3/calculatehistogram.py:214
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler3/calculatemoments.py:243
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:215
↓ 1 callersMethodrun_image
Run measurements on image
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:248
↓ 1 callersMethodrun_image
Run measurements on image
active_plugins/enhancedmeasuretexture.py:948
↓ 1 callersMethodrun_image
(self, image, workspace)
active_plugins/addnoise.py:210
↓ 1 callersMethodrun_image
Run measurements on image
active_plugins/calculatemoments.py:290
↓ 1 callersMethodrun_image_gabor
(self, image_name, scale, workspace)
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:944
↓ 1 callersMethodrun_image_gabor
(self, image_name, scale, workspace)
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:943
↓ 1 callersMethodrun_image_gabor
(self, image_name, scale, workspace)
active_plugins/enhancedmeasuretexture.py:1132
↓ 1 callersMethodrun_image_tamura
Run measurements on image
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:804
↓ 1 callersMethodrun_image_tamura
Run measurements on image
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:803
↓ 1 callersMethodrun_image_tamura
Run measurements on image
active_plugins/enhancedmeasuretexture.py:965
↓ 1 callersMethodrun_local_otsu_2
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:634
↓ 1 callersMethodrun_local_otsu_2
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:643
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