- get() - Method in class ch.epfl.biop.imaris.ItemQuery
-
- get() - Method in class ch.epfl.biop.imaris.StatsQuery
-
Heavy lifting function that performs the requested operation and returns a table It is rather naive.
- getAll(String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get all items of the requested type
- getAllSpots() - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get all spots objects in the main scene as a list
- getAllSurfaces() - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get all surfaces objects in the main scene as a list
- getBitDepth(IDataSetPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Returns bitdepth of a dataset.
- getColorFromInt(int) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Recover a Color for use to set ImagePlus LUTs
- getColorIntFromIntArray(int[]) - Static method in class ch.epfl.biop.imaris.EasyXT
-
recover an RGB color for use with ImageJ from a 3 element (R,G,B) array
- getCurrentDataset() - Static method in class ch.epfl.biop.imaris.EasyXT
-
Convenience method to return the currently active dataset
- getDownsampled(double) - Method in class ch.epfl.biop.imaris.ImarisCalibration
-
- getImagePlus(IDataSetPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Returns an ImagePlus image of a dataset TODO : add a way to select only a subpart of it
- getImaris() - Static method in class ch.epfl.biop.imaris.EasyXT
-
Returns instance of Imaris App
- GetImarisDatasetCommand - Class in ch.epfl.biop.imaris.command
-
- GetImarisDatasetCommand() - Constructor for class ch.epfl.biop.imaris.command.GetImarisDatasetCommand
-
- getItem(String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Return the first item with the selected name.
- getItem(String, int) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Returns nth item of a given type
- getName(IDataItemPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get the name of the requested item, to avoid using GetName()
- getName() - Method in class ch.epfl.biop.imaris.ItemQuery
-
- getOpenImageName() - Static method in class ch.epfl.biop.imaris.EasyXT
-
- getParent() - Method in class ch.epfl.biop.imaris.ItemQuery
-
- getPosition() - Method in class ch.epfl.biop.imaris.ItemQuery
-
- getSpots(String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get the first spots object with the given name
- getSpots(int) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get the n-th spots object in the scene
- getStatistics(IDataItemPrx, String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
returns the selected statistic from the selected item
- getStatistics(IDataItemPrx, String, Integer) - Static method in class ch.epfl.biop.imaris.EasyXT
-
returns only the selected statistic at the selected channel Careful.
- getStatistics(IDataItemPrx, List<String>) - Static method in class ch.epfl.biop.imaris.EasyXT
-
returns the selected statistics
- getStatistics(IDataItemPrx, List<String>, Integer) - Static method in class ch.epfl.biop.imaris.EasyXT
-
returns the selected statistics at the selected channel Careful.
- getStatistics(IDataItemPrx, List<String>, List<Integer>) - Static method in class ch.epfl.biop.imaris.EasyXT
-
returns the selected statistics at the selected channels Careful.
- GetStatisticsDemo - Class in ch.epfl.biop.imaris.demo
-
- GetStatisticsDemo() - Constructor for class ch.epfl.biop.imaris.demo.GetStatisticsDemo
-
- GetSurfaceCommand - Class in ch.epfl.biop.imaris.command
-
- GetSurfaceCommand() - Constructor for class ch.epfl.biop.imaris.command.GetSurfaceCommand
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- getSurfaceDataset(ISurfacesPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
- getSurfaceDataset(ISurfacesPrx, double, int) - Static method in class ch.epfl.biop.imaris.EasyXT
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- getSurfaceMask(ISurfacesPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
- getSurfaceMask(ISurfacesPrx, int) - Static method in class ch.epfl.biop.imaris.EasyXT
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- getSurfaceMask(ISurfacesPrx, double, int) - Static method in class ch.epfl.biop.imaris.EasyXT
-
- getSurfaces(String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get the first surfaces object with the given name
- getSurfaces(int) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Get the first surfaces object with the given name
- getType() - Method in class ch.epfl.biop.imaris.ItemQuery
-
- saveImage(File, String) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Saves the current imaris scene to an imaris file
- saveImage(File) - Static method in class ch.epfl.biop.imaris.EasyXT
-
- selectChannel(Integer) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to select the channel from which to get statistics from
Careful.
- selectChannels(List<Integer>) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to set a list of channels from which to get statistics from
Careful.
- selectId(Integer) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows for the selection of a specific ID.
- selectIds(List<Integer>) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to set a list of IDs from which to get statistics from
- selectStatistic(String) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to select the name of the statistic to export.
- selectStatistics(List<String>) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to set a list of IDs from which to get statistics from
- selectTime(Integer) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to select the timepoint of the statistics to export.
- selectTimes(List<Integer>) - Method in class ch.epfl.biop.imaris.StatsQuery
-
Allows to set a list of timepoints from which to get statistics from
Careful.
- SendNewSurfaceDemo - Class in ch.epfl.biop.imaris.demo
-
- SendNewSurfaceDemo() - Constructor for class ch.epfl.biop.imaris.demo.SendNewSurfaceDemo
-
- setColor(Integer[]) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setColor(Integer[]) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setCurrentDataset(IDataSetPrx) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Convenience method to set/replace the current dataset within the current Imaris scene with the one provided
- setDataSet(IDataSetPrx) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setDataSet(IDataSetPrx) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setDiameter(double) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setFilter(String) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setImagePlus(IDataSetPrx, ImagePlus) - Static method in class ch.epfl.biop.imaris.EasyXT
-
Set data from an ImagePlus image into a dataset TODO : add a way to select only a subpart of it
- setLocalContrastFilterWidth(double) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setLowerThreshold(double) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setName(String) - Method in class ch.epfl.biop.imaris.ItemQuery.ItemQueryBuilder
-
- setName(String) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setName(String) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setParent(IDataContainerPrx) - Method in class ch.epfl.biop.imaris.ItemQuery.ItemQueryBuilder
-
- setPosition(int) - Method in class ch.epfl.biop.imaris.ItemQuery.ItemQueryBuilder
-
- setRegionsThresholdManual(double) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setROI(int[][]) - Method in class ch.epfl.biop.imaris.SpotsDetector.SpotsDetectorBuilder
-
- setROI(int[][]) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setSeedsDiameter(double) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setSeedsFilter(String) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setSmoothingWidth(double) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setSurfaceFilter(String) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- setSurfaceMask(ISurfacesPrx, ImagePlus) - Static method in class ch.epfl.biop.imaris.EasyXT
-
- setType(String) - Method in class ch.epfl.biop.imaris.ItemQuery.ItemQueryBuilder
-
- setUpperThreshold(double) - Method in class ch.epfl.biop.imaris.SurfacesDetector.SurfacesDetectorBuilder
-
- SpotsDetector - Class in ch.epfl.biop.imaris
-
Helper functions for spots detection in Imaris
With the use of a builder pattern, this class combines the following Imaris functions :
- DetectSpots2()
- DetectSpotsRegionGrowing() TODO: implement and explain how the builder switch or not to this function
DetectSpotsWithRegions() not supported -> replaced by DetectSpotsRegionGrowing() T
DetectSpots() obsolete -> replaced by DetectSpots2()
The Builder is tuned to allow for an invisible switch between these functions depending on the builder methods calls
TODO : look at Elliptical spot detection
Authors
Nicolas Chiaruttini, nicolas.chiaruttini@epfl.ch
Olivier Burri, olivier.burri@epfl.ch
BIOP, EPFL, Jan 2020
Useful links:
file:///C:/Program%20Files/Bitplane/Imaris%20x64%209.5.1/html/xtinterface/structImaris_1_1IImageProcessing.html
file:///C:/Program%20Files/Bitplane/Imaris%20x64%209.5.1/html/xtinterface/structImaris_1_1IImageProcessing.html#ae10348d92f0d2df6848ed44253c69391
- SpotsDetector() - Constructor for class ch.epfl.biop.imaris.SpotsDetector
-
- SpotsDetector.SpotsDetectorBuilder - Class in ch.epfl.biop.imaris
-
- StatsQuery - Class in ch.epfl.biop.imaris
-
This class is based on a Builder model to obtain selected statistics from an Imaris cStatisticValues object
It allows for selecting specific item IDs, stat names, channels and timepoints.
- StatsQuery(IDataItemPrx) - Constructor for class ch.epfl.biop.imaris.StatsQuery
-
Constructor for getting selected statistics
- SurfacesDetector - Class in ch.epfl.biop.imaris
-
Helper functions for surface detection in Imaris
With the use of a builder pattern, this class combines the following Imaris functions :
- DetectSurfaces
- DetectSurfaceRegionGrowing TODO: implement and explain how the builder switch or not to this function
- DetectSurfacesRegionGrowingWithUpperThreshold TODO: implement and explain how the builder switch or not to this function
The Builder is tuned to allow for an invisible switch between these functions depending on the builder methods calls
If an upper threshold is set {
calling DetectSurfacesRegionGrowingWithUpperThreshold
} else if any of the seed detection parameters is set {
calling DetectSurfaceRegionGrowing
} else {
calling DetectSurfaces
}
Authors
Nicolas Chiaruttini, nicolas.chiaruttini@epfl.ch
Olivier Burri, olivier.burri@epfl.ch
BIOP, EPFL, Jan 2020
Useful links:
file:///C:/Program%20Files/Bitplane/Imaris%20x64%209.5.1/html/xtinterface/structImaris_1_1IImageProcessing.html
file:///C:/Program%20Files/Bitplane/Imaris%20x64%209.5.1/html/xtinterface/structImaris_1_1IImageProcessing.html#a41275043bc718252958bce85f4d4561a
- SurfacesDetector() - Constructor for class ch.epfl.biop.imaris.SurfacesDetector
-
- SurfacesDetector.SurfacesDetectorBuilder - Class in ch.epfl.biop.imaris
-