MCPcopy Create free account

hub / github.com/CellProfiler/CellProfiler-plugins / functions

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

↓ 1 callersMethodadd_image_cb
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" but
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:112
↓ 1 callersMethodadd_image_cb
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" but
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:177
↓ 1 callersMethodadd_image_cb
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" button for
active_plugins/enhancedmeasuretexture.py:288
↓ 1 callersMethodadd_image_cb
Add an image to the image_groups collection can_delete - set this to False to keep from showing the "remove" button for
active_plugins/calculatemoments.py:196
↓ 1 callersMethodadd_impulse
(self, orig_image, percent)
active_plugins/addnoise.py:254
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" b
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:293
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove"
unmaintained_plugins/CellProfiler2/calculatehistogram.py:128
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" button for
unmaintained_plugins/CellProfiler2/calculatemoments.py:189
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" b
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:292
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove"
unmaintained_plugins/CellProfiler3/calculatehistogram.py:128
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" button for
unmaintained_plugins/CellProfiler3/calculatemoments.py:189
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" b
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:129
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" button for obj
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:194
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" button fo
active_plugins/enhancedmeasuretexture.py:315
↓ 1 callersMethodadd_object_cb
Add an object to the object_groups collection can_delete - set this to False to keep from showing the "remove" button for objects tha
active_plugins/calculatemoments.py:223
↓ 1 callersMethodadd_poisson
(self, orig_image)
active_plugins/addnoise.py:250
↓ 1 callersMethodadd_scale_cb
Add a scale to the scale_groups collection can_delete - set this to False to keep from showing the "remove" butt
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:316
↓ 1 callersMethodadd_scale_cb
Add a scale to the scale_groups collection can_delete - set this to False to keep from showing the "remove" butt
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:315
↓ 1 callersMethodadd_scale_cb
Add a scale to the scale_groups collection can_delete - set this to False to keep from showing the "remove" button for s
active_plugins/enhancedmeasuretexture.py:349
↓ 1 callersMethodadd_threshold_measurements
(self, objname, measurements, local_threshold, global_threshold)
unmaintained_plugins/CellProfiler3/thresh_all.py:674
↓ 1 callersMethodadd_threshold_measurements
(self, objname, measurements, local_threshold, global_threshold)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:683
↓ 1 callersFunctionare_masks_similar
(a, b)
unmaintained_tests/test_identifyyeastcells.py:717
↓ 1 callersMethodbarcodeset
(self, barcodecol, genecol)
unmaintained_plugins/CellProfiler3/callbarcodes.py:497
↓ 1 callersMethodbarcodeset
(self, barcodecol, genecol)
active_plugins/callbarcodes.py:780
↓ 1 callersFunctionbranches
(image)
unmaintained_plugins/CellProfiler3/shollanalysis.py:127
↓ 1 callersFunctionbranches
(image)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:130
↓ 1 callersFunctioncalc_smooth_ranking
(rank_snakes, pf_param_vector)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:113
↓ 1 callersMethodcalculate_centroids
(self, binary_mask)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:134
↓ 1 callersMethodcalculate_distance_to_edge
(self, workspace)
unmaintained_plugins/CellProfiler3/measure_population_context.py:194
↓ 1 callersMethodcalculate_distance_to_edge
(self, workspace)
unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py:197
↓ 1 callersMethodcalculate_entropy
Calculates either the mean, median, or integrated intensity of each bin as per the user's request then calculates the entropy
unmaintained_plugins/CellProfiler3/measureradialentropy.py:152
↓ 1 callersMethodcalculate_entropy
Calculates either the mean, median, or integrated intensity of each bin as per the user's request then calculates the entropy
unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py:154
↓ 1 callersMethodcalculate_population_density
(self, workspace)
unmaintained_plugins/CellProfiler3/measure_population_context.py:126
↓ 1 callersMethodcalculate_population_density
(self, workspace)
unmaintained_plugins/CellProfiler4_autoconverted/measurepopulationcontext.py:129
↓ 1 callersFunctioncallback
(caller, event)
tests/test_runimagejscript.py:37
↓ 1 callersMethodcallonebarcode
(self, measurementdict, measurements, object_name, ncycles)
unmaintained_plugins/CellProfiler3/callbarcodes.py:476
↓ 1 callersMethodcalloneexpISSbarcode
(self, calling_setting_dict, measurements, object_name, ncycles)
active_plugins/callbarcodes.py:673
↓ 1 callersMethodcallonehotbarcode
( self, measurementdict, measurements, object_name, ncycles, objectcount )
active_plugins/callbarcodes.py:748
↓ 1 callersFunctionchan_vese
(image, mask, iterations, alpha, threshold, phi_bound, cfl_factor, sdf_smoothing)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:507
↓ 1 callersFunctionchan_vese
(image, mask, iterations, alpha, threshold, phi_bound, cfl_factor, sdf_smoothing)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:509
↓ 1 callersFunctionchebyshev_transform
(image, M, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:403
↓ 1 callersFunctioncheck_caps_scroll_state
()
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:54
↓ 1 callersFunctioncheck_fourier_transform
(image, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:62
↓ 1 callersFunctioncheck_haar_transform
(image, scale, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:372
↓ 1 callersFunctioncheck_simoncelli_transform_pyramid
(image, scales, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:165
↓ 1 callersFunctioncheck_simoncelli_transform_redundant
(image, scales, mask=None)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:261
↓ 1 callersMethodclear_lists
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:57
↓ 1 callersMethodcluster_seeds
@type seeds: list[Seed]
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:33
↓ 1 callersMethodcompute_typical_deviations
Compute the median absolute temporal difference in each of the features across all tracks :param values_dict: keys are featu
unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py:541
↓ 1 callersMethodcontrast
(self, pixels)
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:714
↓ 1 callersMethodcontrast
(self, pixels)
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:713
↓ 1 callersMethodcontrast
(self, pixels)
active_plugins/enhancedmeasuretexture.py:864
↓ 1 callersFunctionconv_image_repo
(images)
unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py:30
↓ 1 callersFunctionconv_single_image
(image)
unmaintained_plugins/CellProfiler3/cellstar/core/parallel/snake_grow.py:21
↓ 1 callersFunctionconvergence
(p_mask, n_mask, thresh, c)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:723
↓ 1 callersFunctionconvergence
(p_mask, n_mask, thresh, c)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:725
↓ 1 callersMethodcreate
(cls, px, py)
unmaintained_plugins/CellProfiler3/cellstar/utils/index.py:13
↓ 1 callersMethodcreate_all
(gt_snake, grown_pf_snake, params)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_snake.py:32
↓ 1 callersMethodcreate_csv_columns
(self, metadata_features)
active_plugins/boxobjects.py:432
↓ 1 callersMethoddebug_images
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:216
↓ 1 callersMethoddebug_seeds
(self, step)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:221
↓ 1 callersMethoddecode_auto_params_into
Decode automatic parameters from text and apply to self. @param text: parameters denoted as python list @return true if pars
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:101
↓ 1 callersFunctiondefault_config
()
unmaintained_plugins/CellProfiler3/cellstar/core/config.py:9
↓ 1 callersFunctiondilate_big_areas
(mask, min_area_size, dilate_radius)
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:128
↓ 1 callersMethoddirectionality
(self, pixels)
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:722
↓ 1 callersMethoddirectionality
(self, pixels)
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:721
↓ 1 callersMethoddirectionality
(self, pixels)
active_plugins/enhancedmeasuretexture.py:875
↓ 1 callersMethoddisplay
(self, workspace, figure=None)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:571
↓ 1 callersMethoddisplay
(self, workspace, figure=None)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:574
↓ 1 callersFunctiondistance_norm
(fitnesses)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:88
↓ 1 callersFunctiondistance_norm_list
Calculates number of derangments between two sequences @param expected: expected order @param result: given order @return:
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:83
↓ 1 callersFunctiondistance_smooth_norm
Calculates 2-norm from difference in fitness between expected and given snakes @param expected: array of expected fitness @param result:
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:64
↓ 1 callersFunctiondownload_file_from_google_drive
(id, destination)
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:302
↓ 1 callersFunctiondownload_file_from_google_drive
(id, destination)
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:302
↓ 1 callersFunctiondownsample
(image)
unmaintained_plugins/CellProfiler3/transformfilters.py:377
↓ 1 callersFunctiondownsample
(image)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:377
↓ 1 callersFunctiondraw_snakes_on_axes
(snakes, axes, outliers=.1)
unmaintained_plugins/CellProfiler3/cellstar/utils/debug_util.py:182
↓ 1 callersMethodencode_multipart_formdata
(fields, files)
active_plugins/runvista2d.py:642
↓ 1 callersFunctionendpoints
(image)
unmaintained_plugins/CellProfiler3/shollanalysis.py:131
↓ 1 callersFunctionendpoints
(image)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:134
↓ 1 callersFunctionenforce_maximum
(labels, seeds, max_seeds_per_obj)
unmaintained_plugins/CellProfiler3/seedobjects.py:176
↓ 1 callersFunctionenforce_maximum
(labels, seeds, max_seeds_per_obj)
unmaintained_plugins/CellProfiler4_autoconverted/seedobjects.py:178
↓ 1 callersFunctioneuclidean_norm
((x1, y1), (x2, y2))
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:16
↓ 1 callersMethodevaluate_tram_for_split_objects
Compute TrAM results for objects that have split trajectories :param labels_for_split_trajectories: TrackObjects labels for t
unmaintained_plugins/CellProfiler3/measuretrackquality.py:467
↓ 1 callersMethodevaluate_tram_for_split_objects
Compute TrAM results for objects that have split trajectories :param labels_for_split_trajectories: TrackObjects labels for t
unmaintained_plugins/CellProfiler4_autoconverted/measuretrackquality.py:469
↓ 1 callersFunctionexclude_segments
Sets exclusion value for given segments in given image @param image: image from which segments will be excluded @param segments: segments
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:218
↓ 1 callersFunctionextend_slices
(my_slices, extension)
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:142
↓ 1 callersMethodextract_metadata
(self, workspace)
active_plugins/boxobjects.py:445
↓ 1 callersMethodextract_total_mask_of_snake
(snake, tot_shape)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:81
↓ 1 callersMethodfast_local_mean
Compute the local mean using the cumulative sum and matrix arithmetic Lk - the sampling window (I reproduced what you had in the code
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:633
↓ 1 callersMethodfast_local_mean
Compute the local mean using the cumulative sum and matrix arithmetic Lk - the sampling window (I reproduced what you had in the code
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:632
↓ 1 callersMethodfast_local_mean
Compute the local mean using the cumulative sum and matrix arithmetic Lk - the sampling window (I reproduced what you had in the code
active_plugins/enhancedmeasuretexture.py:779
↓ 1 callersFunctionfast_power
(a, n)
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:234
↓ 1 callersFunctionfill_holes
Fills holes in a given mask using iterative close + dilate morphological operations and filtering small patches. @param mask: mask which hole
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:140
↓ 1 callersMethodfilter
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:51
↓ 1 callersMethodfilter_seeds
Ignore seeds that are close image borders or already processed seeds. @param image_shape: (y,x) image size @type seeds: [cell
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:229
↓ 1 callersMethodfilter_snakes
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:212
↓ 1 callersMethodfind_adjacent_by_distance
Return pairs of linear object centers that are deemed adjacent by distance i - i-centers of linear objects j - j-centers of linear ob
unmaintained_plugins/CellProfiler2/identifylinearobjects.py:445
↓ 1 callersMethodfind_adjacent_by_distance
Return pairs of linear object centers that are deemed adjacent by distance i - i-centers of linear objects j - j-centers of linear ob
unmaintained_plugins/CellProfiler3/identifylinearobjects.py:445
↓ 1 callersMethodfind_adjacent_by_distance
Return pairs of linear object centers that are deemed adjacent by distance i - i-centers of linear objects j - j-centers of linear ob
unmaintained_plugins/CellProfiler4_autoconverted/identifylinearobjects.py:447
← previousnext →301–400 of 1,666, ranked by callers