CentromereFinderXMLParameters

These parameters can be added either through the GUI parameter file builder, or by copying and pasting directly into the parameter file between the <root></root> tags and adding the appropriate value.

###File Properties

These parameters are necessary depending on whether a set of images has all color channels in a single file or split into multiple files.

<parameter name="multi_wavelength_file" displayname="Multiple wavelengths in a single file?" type="boolean" value="">
<description>
Specifies whether the files to be processed contain multiple wavelength in one file or split among multiple.  If this is set to false, the parameter channel_name must be added once for each channel (in order, if this matters for the particular method).  Note that if there is only one wavelength being processed, this should be left out completely or set to true so that the program doesn't try to look for multiple files.
</description>
</parameter>

<parameter name="channel_name" displayname="Channel name" type="string" value="">
<description>
If different color channels are not stored in the same file, this parameter specifies a unique tag that identifies the file associated with one color channel.  This parameter should be specified as many times as there are color channels, and the filenames of the different color channels must be exactly the same except for this tag.
</description>
</parameter>

<parameter name="swap_z_t" displayname="Swap z and t dimensions?" type="boolean" value="">
<description>
Certain means of acquiring image series end up with the z-dimension labeled as the t-dimension in the metadata.  This will swap the labels of the two dimensions to fix this.
</description>
</parameter>

<parameter name="process_max_intensity_projections" displayname="Process max intensity projections?" type="boolean" value="">
<description>
Specifies whether to generate temporary maximum intensity projections and run the analysis on those rather than the full image.
</description>
</parameter>

###Centromere Identification

<parameter name="marker_channel_index" displayname="Marker channel index" type="integer" value="">
<description>
The index of the color channel containing the centromere marker to be used for finding centromeres.  This will either be in the order the channels are stored in the file, if all channels are in a single file, or in the order specified by the channel_name parameters.  The indices start at 0.
</description>
</parameter>

<parameter name="maximum_size" displayname="Maximum size" type="integer" value="">
<description>
The maximum number of pixels that can be in a single object before it is either subdivided or discarded.
</description>
</parameter>

<parameter name="minimum_size" displayname="Minimum size" type="integer" value="">
<description>
The minimum number of pixels that can be in a single object before it is discarded.
</description>
</parameter>

###Clustering

<parameter name="use_clustering" displayname="Use clustering?" type="boolean" value="">
<description>
Specifies whether to cluster centromeres into groups corresponding to cells.
</description>
</parameter>

<parameter name="use_basic_clustering" displayname="Use basic clustering only?" type="boolean" value="">
<description>
Two clustering passes are possible; one basic, which works well for widely spaced cells, and one more advanced (but which takes considerably longer) that is useful for dividing centromeres in closely spaced cells.  Specifies whether to use the basic pass only to save time.
</description>
</parameter>

<parameter name="minimum_cluster_size" displayname="Minimum cluster size" type="integer" value="">
<description>
</description>
</parameter>

<parameter name="maximum_clustering_iterations" displayname="Maximum clustering iterations" type="integer" value="">
<description>
</description>
</parameter>

<parameter name="decrease_speckle_background" displayname="Force compensation for punctate background?" type="boolean" value="">
<description>
</description>
</parameter>

<parameter name="maximum_number_of_centromeres" displayname="Maximum number of centromeres" type="integer" value="">
<description>
</description>
</parameter>

###Output

<parameter name="generate_masks" displayname="Generate masks?" type="boolean" value="">
<description>
</description>
</parameter>

<parameter name="generate_values" displayname="Generate values?" type="boolean" value="">
<description>
</description>
</parameter>

###Miscellaneous

<parameter name="max_threads" displayname="Maximum number of threads" type="integer" value="">
<description>
</description>
</parameter>

###Example File

<?xml version="1.0" ?>
<root>
<parameter name="max_size" displayname="Maximum size" type="integer" value="30"></parameter>
<parameter name="min_size" displayname="Minimum size" type="integer" value="5"></parameter>
<parameter name="use_clustering" displayname="Cluster centromeres?" type="boolean" value="true"></parameter>
<parameter name="maximum_clustering_iterations" type="integer" value="1"></parameter>
<parameter name="minimum_cluster_size" type="integer" value="1"></parameter>
<parameter name="decrease_speckle_background" type="boolean" value="false"></parameter>
<parameter name="multi_wavelength_file" displayname="multi_wavelength_file" type="boolean" value="true"></parameter>
<parameter name="max_threads" displayname="Maximum number of execution threads" type="integer" value="2"></parameter>
<parameter name="marker_channel_index" displayname="Marker channel index" type="integer" value="2"></parameter>
</root>