acquifer.ij

Class VirtualPlate

Object

ij.ImageStack

ij.VirtualStack

acquifer.ij.VirtualPlate

public class VirtualPlate
extends ij.VirtualStack

Custom VirtualStack for which each slice is a montage of IM images, downscaled and arranged according to a predefined plate layout.
A VirtualPlate should be constructed from a list of IM images belonging to the same plate acquisition (obviously), but with identical subposition indexes, since a VirtualPlate does not support multiple subpositions.

REMINDER: a VirtualStack has a single dimension slider, it must be transformed to a Hyperstack after, to get up to 3 dimensions sliders (the classical channel, Z, time).
This can be achieved using the instance method toHyperStack() or directly with the static method createHyperStackFromPlateSeries(PlateSeries, Plate, int, boolean).
The slice-order in the VirtualStack must match the order used when converting to a hyperstack (taken care of already).

In this class, we override the method getProcessor(int n) which is responsible for generating the montage for a given slice "on the fly", thus saving memory compared to generating all montage-slices beforehand.
A bunch of other methods from VirtualStack are also overwritten to assure compatibility with most ImageStack/VirtualStack functions in ImageJ.

NOTE : The class expects unsigned 8-bit or 16-bit images as input (default for IM). Although it could be adapted to handle other bitDepth.
The montage image can be converted to 8-bit, which similarly than downscaling reduces the memory footprint of the montage image.
However, when converting to 8-bit, the conversion uses plane-specific intensity normalisation, therefore one cannot compare the intensity between different planes of the hyperstack-montage.

Constructor Summary

Constructors

Constructor and Description
VirtualPlate(acquifer.core.PlateSeries plateSeries, int downScalingFactor) Create a VirtualPlate by concatenating well images.
VirtualPlate(acquifer.core.PlateSeries plateSeries, acquifer.core.Plate plateLayout, int downScalingFactor) Create a VirtualPlate with original bitDepth as the original dataset.
VirtualPlate(acquifer.core.PlateSeries plateSeries, acquifer.core.Plate plateLayout, int downScalingFactor, boolean convertTo8Bit) Create a VirtualPlate from a plateSeries following a plate-layout.

Method Summary

Modifier and Type	Method and Description
void	addSlice(String fileName) Not supported.
static ij.ImagePlus	createHyperStackFromPlateSeries(acquifer.core.PlateSeries plateSeries, acquifer.core.Plate plateLayout, int downScalingFactor) Same as createHyperStackFromPlateSeries(PlateSeries, Plate, int, boolean) using original dataset bitDepth.
static ij.ImagePlus	createHyperStackFromPlateSeries(acquifer.core.PlateSeries plateSeries, acquifer.core.Plate plateLayout, int downScalingFactor, boolean convertTo8Bit) Generate a hyperstack with a VirtualPlate representing a montage of IM images.
void	deleteSlice(int n)
int	getBitDepth()
String	getDirectory()
String	getDirectoryName()
String	getFileName(int n)
int	getHeight()
int	getNumberOfColumns() Return the number of columns in the montage image.
int	getNumberOfRows() Return the number of rows in the montage image.
ij.process.ImageProcessor	getProcessor(int n) Return the ImageProcessor for slice n where 1<=n<=nslices.
int	getSize() Return the number of slices in the VirtualPlate/Stack.
String	getSliceLabel(int n) Return the label of the n-th slice with 1<=n<=nslices.
int	getSubPosition() Return the well-subposition of the images shown in this montage.
int	getWidth()
ij.ImagePlus	toHyperStack() Convert the VirtualPlate to a Hyperstack suitable for display.

Methods inherited from class ij.VirtualStack

addSlice, addSlice, addSlice, deleteLastSlice, getImageArray, getPixels, getProperties, isVirtual, saveChanges, setBitDepth, setIndexes, setPixels, setSliceLabel, size, sortDicom, translate, trim

Methods inherited from class ij.ImageStack

addSlice, addUnsignedShortSlice, convertToFloat, create, create, crop, drawSphere, duplicate, getColorModel, getRoi, getShortSliceLabel, getShortSliceLabel, getSliceLabels, getVoxel, getVoxels, getVoxels, isHSB, isHSB32, isLab, isRGB, setColorModel, setOptions, setProcessor, setRoi, setVoxel, setVoxels, setVoxels, toString, update

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VirtualPlate

public VirtualPlate(acquifer.core.PlateSeries plateSeries,
                    acquifer.core.Plate plateLayout,
                    int downScalingFactor,
                    boolean convertTo8Bit)

Create a VirtualPlate from a plateSeries following a plate-layout.
The montage image will be a black canvas filled with well images where available.
i.e empty plate row/column will result in black image portion in the montage.
To make a montage without the black areas, use the other constructor VirtualPlate(PlateSeries, int).
To create a PlateSeries from a Dataset, use PlateSeries.groupByPlateSeries(dataset).

Parameters:

plateSeries -

plateLayout -

downScalingFactor - value by which width and height are divided to yield a single well-image.
If downScalingFactor = 1 then there is no resizing of the image (not recommended as it might yield large montage images).

convertTo8Bit - convert each image plane to 8-bit before integrating them in the montage.
This reduces the memory footprint of the montage image, but uses plane-specific intensity normalisation, therefore one cannot compare the intensity between different wells of the montage.

VirtualPlate

public VirtualPlate(acquifer.core.PlateSeries plateSeries,
                    acquifer.core.Plate plateLayout,
                    int downScalingFactor)

Create a VirtualPlate with original bitDepth as the original dataset.

VirtualPlate

public VirtualPlate(acquifer.core.PlateSeries plateSeries,
                    int downScalingFactor)

Create a VirtualPlate by concatenating well images.
Contrary to the other constructor with the plate-layout, here empty rows/columns are not included in the montage.

Method Detail

getNumberOfRows

public int getNumberOfRows()

Return the number of rows in the montage image.

getNumberOfColumns

public int getNumberOfColumns()

Return the number of columns in the montage image.

getWidth

public int getWidth()

Overrides:

getWidth in class ij.ImageStack

getHeight

public int getHeight()

Overrides:

getHeight in class ij.ImageStack

getSize

public int getSize()

Return the number of slices in the VirtualPlate/Stack.

Overrides:

getSize in class ij.VirtualStack

getBitDepth

public int getBitDepth()

Overrides:

getBitDepth in class ij.VirtualStack

getDirectory

public String getDirectory()

Overrides:

getDirectory in class ij.VirtualStack

getDirectoryName

public String getDirectoryName()

getFileName

public String getFileName(int n)

Overrides:

getFileName in class ij.VirtualStack

getSubPosition

public int getSubPosition()

Return the well-subposition of the images shown in this montage.

addSlice

public void addSlice(String fileName)

Not supported.

Overrides:

addSlice in class ij.VirtualStack

deleteSlice

public void deleteSlice(int n)

Overrides:

deleteSlice in class ij.VirtualStack

getProcessor

public ij.process.ImageProcessor getProcessor(int n)

Return the ImageProcessor for slice n where 1<=n<=nslices.
The returned ImageProcessor is generated on the fly, which allows saving RAM and provides fast loading compared to storing all the planes for the montage.

Overrides:

getProcessor in class ij.VirtualStack

getSliceLabel

public String getSliceLabel(int n)

Return the label of the n-th slice with 1<=n<=nslices.

Overrides:

getSliceLabel in class ij.VirtualStack

createHyperStackFromPlateSeries

public static ij.ImagePlus createHyperStackFromPlateSeries(acquifer.core.PlateSeries plateSeries,
                                                           acquifer.core.Plate plateLayout,
                                                           int downScalingFactor,
                                                           boolean convertTo8Bit)
                                                    throws IOException

Generate a hyperstack with a VirtualPlate representing a montage of IM images.
The title of the ImagePlus holding the hyperstack is the image directory followed by the subposition.

Throws:

IOException

createHyperStackFromPlateSeries

public static ij.ImagePlus createHyperStackFromPlateSeries(acquifer.core.PlateSeries plateSeries,
                                                           acquifer.core.Plate plateLayout,
                                                           int downScalingFactor)
                                                    throws IOException

Same as createHyperStackFromPlateSeries(PlateSeries, Plate, int, boolean) using original dataset bitDepth.

Throws:

IOException

toHyperStack

public ij.ImagePlus toHyperStack()

Convert the VirtualPlate to a Hyperstack suitable for display.
The title of the image window is "directory - SubPosition:x".
This method also sets the LUT of the imp channel, according to the settings saved in Preference.
Additionally the pixel is populated as part of the image Calibration if the dataset is made of tiff images, which header contains the pixel size.
The hyperstack is backed by a VirtualPlate, it is thus a Virtual Stack.