- saturation - Static variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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Percentage of pixels that will be saturated when enhancing the contrast.
- saveDefaultParameters() - Method in class acquifer.ij.BatchDialog
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This function save the default GUI parameters, expected in this order
- Input directory
- Channel selector
- Z-slice selector
- Timepoint selector
- well subposition
- well selections
It also saves the last visited/default directory for the OpenDialog.
- saveParameters() - Method in class acquifer.ij.im.plugins.HyperstackBrowser
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Dont do anything.
- saveProjection - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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If the projection should be saved
- saveStack - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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If yes or no, the stack should be saved.
- saveWellCheckboxState() - Method in class acquifer.ij.BatchDialog
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Save the checkboxes states in persistence for the full checkbox group as a string "True, True, False..."
- setBitDepth(int) - Method in class acquifer.ij.VirtualImageSeries
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- setCalibrationPixelSizeXY(ImagePlus, FileInfo) - Static method in class acquifer.ij.Utils
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Populate the pixelWidth and pixelHeight of an ImagePlus based on tiffMetadata.
- setChannelLut(int, String) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set the Look Up Table (LUT) for a given channel of the microscope.
- setContrastSaturation(double) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set the saturation used to automatically enhance contrast of stacks generated with the plugin.
- setDefaultChannelsLut(String[]) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set the Look Up Tables used to rendered the IM channels in hyperstacks.
- setDefaultDisplayMagnification(double) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set default magnification used by the hyperstack plugin for the display of new images.
- setDefaultSliderPositions(ImagePlus) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set the slider position to the default values defined in settings
- setHyperStackDisplayMode(Hyperstack_Maker.DisplayMode) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Set the default display mode for hyperstack when nChannels>1.
- setLUTs(ImagePlus, Collection<Integer>) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Apply the LUT defined in settings to the channels of the provided imp (for ImageJ>=1.53).
- setOKLabel(String) - Method in class acquifer.ij.BatchDialog
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- setOKLabel(String) - Method in class acquifer.ij.im.plugins.HyperstackBrowser
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Does not do anything.
- showDialog() - Method in class acquifer.ij.BatchDialog
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Reorganise the GUI layout with left/right panels.
- showHyperStacks(Dataset, MetadataParser) - Static method in class acquifer.ij.im.plugins.Hyperstack_Maker
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Display the hyperstack(s) of a dataset.
- showHyperStacks(Dataset) - Static method in class acquifer.ij.im03.plugins.Hyperstack_Maker
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Make a list of hyperstack (as ImagePlus) from a dataset.
- showHyperStacks(Dataset) - Static method in class acquifer.ij.im04.plugins.Hyperstack_Maker
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Make a list of hyperstack (as ImagePlus) from a dataset.
- showProjection - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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Show stack projection (yes/no)
- showProjectionTickbox - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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If a tick box should be shown in the GUI to ask the user about yes/no project stack
- showStack - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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If yes or no the stack should be shown
- stack - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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Stack/hyperstack generated by the plugin at each iteration (each well).
- stackDir - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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Where the stack should be saved if saveStack is true.
- startSlice - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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- stopSlice - Variable in class acquifer.ij.im.plugins.Hyperstack_Maker
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