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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
↓ 1 callers
Method
run_local_otsu_3b
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:651
↓ 1 callers
Method
run_local_otsu_3b
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:660
↓ 1 callers
Method
run_local_otsu_3f
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:642
↓ 1 callers
Method
run_local_otsu_3f
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:651
↓ 1 callers
Method
run_mce
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:605
↓ 1 callers
Method
run_mce
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:614
↓ 1 callers
Method
run_object
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler2/calculatehistogram.py:231
↓ 1 callers
Method
run_object
(self, image_name, object_name, workspace)
unmaintained_plugins/CellProfiler2/calculatemoments.py:257
↓ 1 callers
Method
run_object
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler3/calculatehistogram.py:231
↓ 1 callers
Method
run_object
(self, image_name, object_name, workspace)
unmaintained_plugins/CellProfiler3/calculatemoments.py:257
↓ 1 callers
Method
run_object
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler4_autoconverted/calculatehistogram.py:232
↓ 1 callers
Method
run_object
(self, image_name, object_name, workspace)
unmaintained_plugins/CellProfiler4_autoconverted/calculatemoments.py:262
↓ 1 callers
Method
run_object
(self, image_name, object_name, workspace)
active_plugins/calculatemoments.py:303
↓ 1 callers
Method
run_one
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:557
↓ 1 callers
Method
run_one
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:556
↓ 1 callers
Method
run_one
Run, computing the area measurements for a single map of objects
active_plugins/enhancedmeasuretexture.py:689
↓ 1 callers
Method
run_one_gabor
(self, image_name, object_name, scale, workspace)
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:898
↓ 1 callers
Method
run_one_gabor
(self, image_name, object_name, scale, workspace)
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:897
↓ 1 callers
Method
run_one_gabor
(self, image_name, object_name, scale, workspace)
active_plugins/enhancedmeasuretexture.py:1084
↓ 1 callers
Method
run_one_step
(self, step)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:226
↓ 1 callers
Method
run_one_tamura
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler2/enhancedmeasuretexture.py:832
↓ 1 callers
Method
run_one_tamura
Run, computing the area measurements for a single map of objects
unmaintained_plugins/CellProfiler3/enhancedmeasuretexture.py:831
↓ 1 callers
Method
run_one_tamura
Run, computing the area measurements for a single map of objects
active_plugins/enhancedmeasuretexture.py:994
↓ 1 callers
Method
run_robustbackground
(self, image, workspace, module)
unmaintained_plugins/CellProfiler3/thresh_all.py:660
↓ 1 callers
Method
run_robustbackground
(self, image, workspace, module)
unmaintained_plugins/CellProfiler4_autoconverted/testallthresholds.py:669
↓ 1 callers
Function
run_singleprocess
:param gt_snakes: gt snakes label image :param precision: if initial_params is None then it is used to calculate parameters :param avg_ce
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_rank_process.py:176
↓ 1 callers
Function
save_response_content
(response, destination)
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:328
↓ 1 callers
Function
save_response_content
(response, destination)
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:328
↓ 1 callers
Method
save_result
(files, tmpdir)
active_plugins/runvista2d.py:622
↓ 1 callers
Function
seed_is_new
(seed, current_seeds, distance)
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:279
↓ 1 callers
Method
segmentation
(self, normalized_image, background_pixels, ignore_mask_pixels=None)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:811
↓ 1 callers
Method
segmentation
(self, normalized_image, background_pixels, ignore_mask_pixels=None)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:814
↓ 1 callers
Method
set_erosion
(self, size)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_snake.py:137
↓ 1 callers
Function
set_image_border
Sets pixel values at image borders to given value @param image: image that borders will be set to given value @param val: value to be s e
unmaintained_plugins/CellProfiler3/cellstar/utils/image_util.py:298
↓ 1 callers
Method
set_params_from_ui
(self, params)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:664
↓ 1 callers
Method
set_params_from_ui
(self, params)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:667
↓ 1 callers
Method
set_ui_from_precision
(self, ui_precision)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:728
↓ 1 callers
Method
set_ui_from_precision
(self, ui_precision)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:731
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler3/nucleaizer.py:84
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler3/randomwalkeralgorithm.py:51
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:425
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:215
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler3/histogramequalization.py:55
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler4_autoconverted/nucleaizer.py:87
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler4_autoconverted/randomwalkeralgorithm.py:53
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:428
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:217
↓ 1 callers
Method
settings
(self)
unmaintained_plugins/CellProfiler4_autoconverted/histogramequalization.py:57
↓ 1 callers
Method
settings
(self)
active_plugins/distancetransform.py:63
↓ 1 callers
Method
settings
(self)
active_plugins/pixelshuffle.py:44
↓ 1 callers
Method
settings
(self)
active_plugins/histogrammatching.py:79
↓ 1 callers
Method
settings
(self)
active_plugins/histogramequalization.py:114
↓ 1 callers
Function
shiftb
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:718
↓ 1 callers
Function
shiftb
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:720
↓ 1 callers
Function
shiftd
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:698
↓ 1 callers
Function
shiftd
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:700
↓ 1 callers
Function
shiftf
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:714
↓ 1 callers
Function
shiftf
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:716
↓ 1 callers
Function
shiftl
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:702
↓ 1 callers
Function
shiftl
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:704
↓ 1 callers
Function
shiftr
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:706
↓ 1 callers
Function
shiftr
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:708
↓ 1 callers
Function
shiftu
(m)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:710
↓ 1 callers
Function
shiftu
(m)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:712
↓ 1 callers
Function
sholl
(image, radius, step)
unmaintained_plugins/CellProfiler3/shollanalysis.py:34
↓ 1 callers
Function
sholl
(image, radius, step)
unmaintained_plugins/CellProfiler4_autoconverted/shollanalysis.py:37
↓ 1 callers
Function
show_progress
(current_distance, calculation)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:61
↓ 1 callers
Function
single_mask_to_snake
(bool_mask, seed=None)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_runner.py:25
↓ 1 callers
Method
slice_and_measure_intensity
For each object, iterate over the pixels that make up the object, assign them to a bin, then call calculate_entropy and return it to run. Nee
unmaintained_plugins/CellProfiler3/measureradialentropy.py:117
↓ 1 callers
Method
slice_and_measure_intensity
For each object, iterate over the pixels that make up the object, assign them to a bin, then call calculate_entropy and return it to run. Nee
unmaintained_plugins/CellProfiler4_autoconverted/measureradialentropy.py:119
↓ 1 callers
Method
smooth_contour
Smoothing contour using greedy length cut. Rotating from min radius clockwise and anti. @type radius: np.ndarray @param max_d
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:201
↓ 1 callers
Function
snakes_fitness
(gt_snake_seed_pairs, images, parameters, pf_param_vector, debug=False)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_process.py:104
↓ 1 callers
Method
snakes_from_seeds
(self)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:175
↓ 1 callers
Method
start
(self)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:1134
↓ 1 callers
Function
sub2ind
(dim, (x, y))
unmaintained_plugins/CellProfiler3/cellstar/utils/calc_util.py:94
↓ 1 callers
Function
sussman
(D, dt)
unmaintained_plugins/CellProfiler3/activecontourmodel.py:642
↓ 1 callers
Function
sussman
(D, dt)
unmaintained_plugins/CellProfiler4_autoconverted/activecontourmodel.py:644
↓ 1 callers
Function
unet_classify
(model, input_image, resize_to_model=True)
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:196
↓ 1 callers
Function
unet_classify
(model, input_image, resize_to_model=True)
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:196
↓ 1 callers
Function
unet_initialize
initialize a unet of size shape, with optiaonel size adjustment if necessary Args: input_shape: tuple automated_shapte_adjustem
unmaintained_plugins/CellProfiler3/classifypixelsunet.py:118
↓ 1 callers
Function
unet_initialize
initialize a unet of size shape, with optiaonel size adjustment if necessary Args: input_shape: tuple automated_shapte_adjustem
unmaintained_plugins/CellProfiler4_autoconverted/classifypixelsunet.py:118
↓ 1 callers
Method
update_params
(self, new_params)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:1119
↓ 1 callers
Method
update_params
(self, new_params)
unmaintained_plugins/CellProfiler4_autoconverted/identifyyeastcells.py:1122
↓ 1 callers
Function
upsample
(image)
unmaintained_plugins/CellProfiler3/transformfilters.py:387
↓ 1 callers
Function
upsample
(image)
unmaintained_plugins/CellProfiler4_autoconverted/transformfilters.py:387
↓ 1 callers
Function
wait_for_server_startup
Helper method that blocks until the timeout value is reached, or the ImageJ server becomes available for connection. Parameters ----
active_plugins/cpij/server.py:459
Method
PSDtoPolar
(PSD_cartesian, frequencies_x, frequencies_y, anglerange)
unmaintained_plugins/CellProfiler3/spectralanalysis.py:114
Method
PSDtoPolar
(PSD_cartesian, frequencies_x, frequencies_y, anglerange)
unmaintained_plugins/CellProfiler4_autoconverted/spectralanalysis.py:112
Method
__call__
(self, **kwargs)
unmaintained_plugins/CellProfiler3/cellstar/parameter_fitting/pf_auto_params.py:56
Method
__eq__
(self, other)
unmaintained_plugins/CellProfiler3/cellstar/core/point.py:28
Method
__init__
(self, target, callback, *args)
unmaintained_plugins/CellProfiler3/identifyyeastcells.py:1109
Method
__init__
(self, segmentation_precision=9, avg_cell_diameter=35)
unmaintained_plugins/CellProfiler3/cellstar/segmentation.py:27
Method
__init__
@type x: int @type y: int
unmaintained_plugins/CellProfiler3/cellstar/core/point.py:17
Method
__init__
(self, avg_cell_diameter, points_number, step, max_size)
unmaintained_plugins/CellProfiler3/cellstar/core/polar_transform.py:85
Method
__init__
@type images: core.image_repo.ImageRepo @type parameters: dict
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:19
Method
__init__
(self, size=10)
unmaintained_plugins/CellProfiler3/cellstar/core/seeder.py:288
Method
__init__
@param image: 0-1 float array @type image: np.ndarray @type parameters: dict
unmaintained_plugins/CellProfiler3/cellstar/core/image_repo.py:125
Method
__init__
@type x: int @type y: int
unmaintained_plugins/CellProfiler3/cellstar/core/seed.py:19
Method
__init__
@type seed: Seed @type images: core.image_repo.ImageRepo @type points: list[Point] @type parameters: dict
unmaintained_plugins/CellProfiler3/cellstar/core/snake.py:54
Method
__init__
@type parameters: dict @type images: core.image_repo.ImageRepo
unmaintained_plugins/CellProfiler3/cellstar/core/snake_filter.py:22
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