The final product of the **Images** module is a file list in which any files that are not intended for further processing have been removed, whether manually or using filtering. This list will be used when collecting metadata (if desired) and when assembling the image sets in NamesAndTypes. The list can be filtered further in NamesAndTypes to specify, for example, that a subset of these images represents a particular wavelength. .. _here: http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html .. _“lossy”: http://www.techterms.com/definition/lossy .. _“lossless”: http://www.techterms.com/definition/lossless """.format( **{ "IMG_PANEL_BLANK": _help.__image_resource('Images_FilelistPanel_Blank.png'), "IMG_PANEL_FILLED": _help.__image_resource('Images_FilelistPanel_Filled.png') }) FILTER_CHOICE_NONE = "No filtering" FILTER_CHOICE_IMAGES = "Images only" FILTER_CHOICE_CUSTOM = "Custom" FILTER_CHOICE_ALL = [ FILTER_CHOICE_NONE, FILTER_CHOICE_IMAGES, FILTER_CHOICE_CUSTOM ] FILTER_DEFAULT = 'and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")' class Images(cpm.Module):
- *Group\_Index:* The index of each imaget set within each grouping, as defined by the *Group\_Number*. These are written to the per-image table. Technical notes ^^^^^^^^^^^^^^^ To perform grouping, only one analysis worker (i.e., copy of CellProfiler) will be allocated to handle each group. This means that you may have multiple workers created (as set under the Preferences), but only a subset of them may actually be active, depending on the number of groups you have. """.format( **{ "GROUPS_DISPLAY_TABLE": _help.__image_resource('Groups_ExampleDisplayTable.png') }) class Groups(cpm.Module): variable_revision_number = 2 module_name = "Groups" category = "File Processing" IDX_GROUPING_METADATA_COUNT = 1 def create_settings(self): self.pipeline = None self.metadata_keys = {} module_explanation = [
tracking of objects”, Proceedings from XV Brazilian Symposium on Computer Graphics and Image Processing, 2002. `(pdf)`_ - Principles of Digital Image Processing: Core Algorithms (Undergraduate Topics in Computer Science): `Section 2.4.3 - Statistical shape properties`_ - Chrystal P (1885), “On the problem to construct the minimum circle enclosing n given points in a plane”, *Proceedings of the Edinburgh Mathematical Society*, vol 3, p. 30 .. _(pdf): http://sibgrapi.sid.inpe.br/col/sid.inpe.br/banon/2002/10.23.11.34/doc/35.pdf .. _Section 2.4.3 - Statistical shape properties: http://www.scribd.com/doc/58004056/Principles-of-Digital-Image-Processing#page=49 .. |MOSS_image0| image:: {ECCENTRICITY_ICON} """.format( **{ "ECCENTRICITY_ICON": _help.__image_resource("MeasureObjectSizeShape_Eccentricity.png") }) """The category of the per-object measurements made by this module""" AREA_SHAPE = 'AreaShape' """Calculate Zernike features for N,M where N=0 through ZERNIKE_N""" ZERNIKE_N = 9 F_AREA = "Area" F_ECCENTRICITY = 'Eccentricity' F_SOLIDITY = 'Solidity' F_EXTENT = 'Extent' F_CENTER_X = 'Center_X' F_CENTER_Y = 'Center_Y' F_CENTER_Z = 'Center_Z' F_EULER_NUMBER = 'EulerNumber' F_PERIMETER = 'Perimeter'
combinations of the metadata tags specified. These are written to the per-image table. - *Group\_Index:* The index of each image set within each grouping, as defined by the *Group\_Number*. These are written to the per-image table. Technical notes ^^^^^^^^^^^^^^^ To perform grouping, only one analysis worker (i.e., copy of CellProfiler) will be allocated to handle each group. This means that you may have multiple workers created (as set under the Preferences), but only a subset of them may actually be active, depending on the number of groups you have. """.format(**{ "GROUPS_DISPLAY_TABLE": _help.__image_resource('Groups_ExampleDisplayTable.png') }) class Groups(cpm.Module): variable_revision_number = 2 module_name = "Groups" category = "File Processing" IDX_GROUPING_METADATA_COUNT = 1 def create_settings(self): self.pipeline = None self.metadata_keys = {} module_explanation = [ "The %s module optionally allows you to split your list of images into image subsets" % self.module_name,
What do I get as output? ^^^^^^^^^^^^^^^^^^^^^^^^ The final product of the **Images** module is a file list in which any files that are not intended for further processing have been removed, whether manually or using filtering. This list will be used when collecting metadata (if desired) and when assembling the image sets in NamesAndTypes. The list can be filtered further in NamesAndTypes to specify, for example, that a subset of these images represents a particular wavelength. .. _here: http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html .. _“lossy”: http://www.techterms.com/definition/lossy .. _“lossless”: http://www.techterms.com/definition/lossless """.format(**{ "IMG_PANEL_BLANK": _help.__image_resource('Images_FilelistPanel_Blank.png'), "IMG_PANEL_FILLED": _help.__image_resource('Images_FilelistPanel_Filled.png') }) FILTER_CHOICE_NONE = "No filtering" FILTER_CHOICE_IMAGES = "Images only" FILTER_CHOICE_CUSTOM = "Custom" FILTER_CHOICE_ALL = [FILTER_CHOICE_NONE, FILTER_CHOICE_IMAGES, FILTER_CHOICE_CUSTOM] FILTER_DEFAULT = 'and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")' class Images(cpm.Module): variable_revision_number = 2
- Rocha L, Velho L, Carvalho PCP, “Image moments-based structuring and tracking of objects”, Proceedings from XV Brazilian Symposium on Computer Graphics and Image Processing, 2002. `(pdf)`_ - Principles of Digital Image Processing: Core Algorithms (Undergraduate Topics in Computer Science): `Section 2.4.3 - Statistical shape properties`_ - Chrystal P (1885), “On the problem to construct the minimum circle enclosing n given points in a plane”, *Proceedings of the Edinburgh Mathematical Society*, vol 3, p. 30 .. _(pdf): http://sibgrapi.sid.inpe.br/col/sid.inpe.br/banon/2002/10.23.11.34/doc/35.pdf .. _Section 2.4.3 - Statistical shape properties: http://www.scribd.com/doc/58004056/Principles-of-Digital-Image-Processing#page=49 .. |MOSS_image0| image:: {ECCENTRICITY_ICON} """.format(**{ "ECCENTRICITY_ICON": _help.__image_resource("MeasureObjectSizeShape_Eccentricity.png") }) """The category of the per-object measurements made by this module""" AREA_SHAPE = 'AreaShape' """Calculate Zernike features for N,M where N=0 through ZERNIKE_N""" ZERNIKE_N = 9 F_AREA = "Area" F_ECCENTRICITY = 'Eccentricity' F_SOLIDITY = 'Solidity' F_EXTENT = 'Extent' F_CENTER_X = 'Center_X' F_CENTER_Y = 'Center_Y' F_CENTER_Z = 'Center_Z'