Inheritance diagram for BioCore.BioImage:

Classes
class	ImageJDesc

class	WellPlate

Public Types
enum	ImageType

Public Member Functions
BioImage	Copy (bool rois)

BioImage	Copy ()

double	GetLevelDownsample (int level)
	Get the downsampling factor of a given level. More...

int	LevelFromResolution (double Resolution)
	Returns the level of a given resolution. More...

double	GetUnitPerPixel (int level)
	Get Unit Per Pixel for pyramidal images. More...

async void	UpdateBuffersPyramidal ()
	Updates the Buffers based on current pyramidal origin and resolution. More...

void	To8Bit ()

void	To16Bit ()

void	To24Bit ()

void	To32Bit ()

void	To48Bit ()

void	RotateFlip (RotateFlipType rot)

void	Bake (int rmin, int rmax, int gmin, int gmax, int bmin, int bmax)

void	Bake (IntRange rf, IntRange gf, IntRange bf)

void	UpdateCoords ()

void	UpdateCoords (int sz, int sc, int st)

void	UpdateCoords (int sz, int sc, int st, string order)

double	ToImageSizeX (double d)

double	ToImageSizeY (double d)

double	ToImageSpaceX (double x)

double	ToImageSpaceY (double y)

PointD	ToImageSpace (PointD p)

PointD[]	ToImageSpace (List< PointD > p)

PointF[]	ToImageSpace (PointF[] p)

System.Drawing.RectangleF	ToImageSpace (RectangleD p)

PointD	ToStageSpace (PointD p)

RectangleD	ToStageSpace (RectangleD p)

PointD[]	ToStageSpace (PointD[] p)

PointD	ToStageSpace (PointD p, int resolution)

	BioImage (string file)

BioImage[]	SplitChannels ()

Image	GetImageByCoord (int z, int c, int t)

Bitmap	GetBitmap (int z, int c, int t)

int	GetIndex (int ix, int iy)

int	GetIndexRGB (int ix, int iy, int index)

ushort	GetValue (ZCTXY coord)

ushort	GetValueRGB (ZCTXY coord, int index)

ushort	GetValue (ZCT coord, int x, int y)

ushort	GetValue (int z, int c, int t, int x, int y)

ushort	GetValueRGB (ZCT coord, int x, int y, int RGBindex)

ushort	GetValueRGB (int z, int c, int t, int x, int y, int RGBindex)

void	SetValue (ZCTXY coord, ushort value)

void	SetValue (int x, int y, int ind, ushort value)

void	SetValue (int x, int y, ZCT coord, ushort value)

void	SetValueRGB (ZCTXY coord, int RGBindex, ushort value)

Bitmap	GetBitmap (ZCT coord)

Bitmap	GetFiltered (ZCT coord, IntRange r, IntRange g, IntRange b)

Bitmap	GetFiltered (int ind, IntRange r, IntRange g, IntRange b)

Bitmap	GetChannelImage (int ind, RGB rGB)

Bitmap	GetEmission (ZCT coord, IntRange rf, IntRange gf, IntRange bf)

Bitmap	GetRGBBitmap (ZCT coord, IntRange rf, IntRange gf, IntRange bf)

List< ROI >	GetAnnotations (ZCT coord)

List< ROI >	GetAnnotations (int Z, int C, int T)

Bitmap	GetTileRGB (ZCT coord, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY)

void	StackThreshold (bool bit16)

void	Update ()
	It updates the current object. More...

void	Dispose ()

override string	ToString ()

Static Public Member Functions
static BioImage	Copy (BioImage b, bool rois)

static BioImage	Copy (BioImage b)

static BioImage	CopyInfo (BioImage b, bool copyAnnotations, bool copyChannels)

static void	OpenVips (BioImage b, int pagecount)

static void	OpenVip (BioImage b, int pagenumber, int x, int y, int w, int h)

static PointD	ToStageSpace (PointD p, double physicalSizeX, double physicalSizeY, double volumeX, double volumeY)

static RectangleD	ToStageSpace (RectangleD p, double physicalSizeX, double physicalSizeY, double volumeX, double volumeY)

static PointD[]	ToStageSpace (PointD[] p, double physicalSizeX, double physicalSizeY, double volumeX, double volumeY)

static BioImage	Substack (BioImage orig, int ser, int zs, int ze, int cs, int ce, int ts, int te)

static BioImage	MergeChannels (BioImage b2, BioImage b)

static BioImage	MergeChannels (string bname, string b2name)

static BioImage	MergeZ (BioImage b)

static BioImage	MergeT (BioImage b)

static BioImage[]	SplitChannels (BioImage bb)

static BioImage[]	SplitChannels (string name)

static void	Initialize ()

static void	SaveFile (string file, string ID)

static void	SaveSeries (string[] files, string ID)

static BioImage[]	OpenSeries (string file)

static BioImage	OpenFile (string file)

static BioImage	OpenFile (string file, int series, bool newTab)

static BioImage	OpenFile (string file, int series, bool newTab, bool addToImages, bool tile, int x, int y, int w, int h)

static bool	isTiffSeries (string file)

static bool	isOME (string file)

static bool	isOMESeries (string file)

static void	SaveOME (string file, string ID)

static void	SaveOMESeries (string[] files, string f, bool planes)

static void	SaveOMESeries (BioImage[] bms, string f, bool planes)

static void	SaveOMEStiched (BioImage[] bms, string file, string compression)

static void	SaveOMEPyramidal (BioImage[] bms, string file, Enums.ForeignTiffCompression compression, int compressionLevel)
	The function `SaveOMEPyramidal` saves a collection of BioImages as a pyramidal OME-TIFF file. More...

static BioImage	OpenOME (string file)

static BioImage	OpenOME (string file, int serie, bool newTab, bool addToImages)

static BioImage	FilesToStack (string[] files, int sizeZ, int sizeC, int sizeT)

static BioImage	FolderToStack (string path)

static BioImage	OpenOME (string file, int serie, bool tab, bool addToImages, bool tile, int tilex, int tiley, int tileSizeX, int tileSizeY, bool useOpenSlide=true)

static int	FindFocus (BioImage im, int Channel, int Time)

static BufferInfo	ExtractRegionFromTiledTiff (BioImage b, int x, int y, int width, int height, int res)

static BufferInfo	GetTile (BioImage b, ZCT coord, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY, bool OpenSlide=true)

static BufferInfo	GetTile (BioImage b, int index, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY, bool OpenSlide=true)

static bool	VipsSupport (string file)

static int	GetBitsPerPixel (int bt)

static int	GetBitMaxValue (int bt)

static PixelFormat	GetPixelFormat (int rgbChannelCount, int bitsPerPixel)

static PixelFormat	GetPixelFormat (int rgbChannelCount, ome.xml.model.enums.PixelType px)

static BioImage[]	OpenOMESeries (string file, bool newTab, bool addToImages)

static async Task	OpenAsync (string file, bool OME, bool newtab, bool images, int series)

static async Task	OpenAsync (string[] files, bool OME, bool tab, bool images)

static BioImage	OpenFile (string file, int series, bool tab, bool addToImages)

static async Task	SaveAsync (string file, string id, int serie, bool ome)
	The SaveAsync function saves data to a file asynchronously. More...

static async Task	SaveSeriesAsync (BioImage[] imgs, string file, bool ome)
	The function `SaveSeriesAsync` saves a series of `BioImage` objects to a file asynchronously. More...

static async Task	SavePyramidalAsync (BioImage[] imgs, string file, Enums.ForeignTiffCompression com, int compLevel)
	The function `SavePyramidalAsync` saves an array of `BioImage` objects as a pyramidal TIFF file asynchronously. More...

static void	Open (string file)

static void	Open (string[] files)

static void	Save (string file, string ID)

static BioImage	ImagesToStack (string[] files)

static void	Update (BioImage b)

static int	GetSeriesCount (string file)

static string	OpenXML (string file)

static List< ROI >	OpenOMEROIs (string file, int series)

static string	ROIsToString (List< ROI > Annotations)

static string	ROIToString (ROI an)

static ROI	StringToROI (string sts)

static void	ExportROIsCSV (string filename, List< ROI > Annotations)

static List< ROI >	ImportROIsCSV (string filename)

static void	ExportROIFolder (string path, string filename)

static void	AutoThreshold (BioImage b, bool updateImageStats)

static void	AutoThreshold ()

static void	AutoThresholdThread (BioImage b)

static BioImage	operator/ (BioImage a, float b)

static BioImage	operator* (BioImage a, float b)

static BioImage	operator+ (BioImage a, float b)

static BioImage	operator- (BioImage a, float b)

static BioImage	operator/ (BioImage a, ColorS b)

static BioImage	operator* (BioImage a, ColorS b)

static BioImage	operator+ (BioImage a, ColorS b)

static BioImage	operator- (BioImage a, ColorS b)

Public Attributes
int[,,]	Coords

WellPlate	Plate = null

List< Channel >	Channels = new List<Channel>()

List< Resolution >	Resolutions = new List<Resolution>()

List< BufferInfo >	Buffers = new List<BufferInfo>()

List< ROI >	Annotations = new List<ROI>()

OpenSlideImage	openSlideImage

OpenSlideBase	openSlideBase

SlideBase	slideBase

SlideImage	slideImage

string	filename = ""

string	script = ""

int[]	rgbChannels = new int[3]

int	bitsPerPixel

int	imagesPerSeries = 0

int	seriesCount = 1

double	frameInterval = 0

bool	littleEndian = false

bool	isGroup = false

long	loadTimeMS = 0

long	loadTimeTicks = 0

bool	selected = false

List< NetVips.Image >	vipPages = new List<NetVips.Image>()

Stopwatch	watch = new Stopwatch()

string	file

bool	Loading = false

ImageReader	imRead = null

Static Public Attributes
static bool	Planes = false

static LevelsLinear	filter8 = new LevelsLinear()

static LevelsLinear16bpp	filter16 = new LevelsLinear16bpp()

static Stopwatch	swatch = new Stopwatch()

const char	NewLine = '\n'

const string	columns = "ROIID,ROINAME,TYPE,ID,SHAPEINDEX,TEXT,S,C,Z,T,X,Y,W,H,POINTS,STROKECOLOR,STROKECOLORW,FILLCOLOR,FONTSIZE\n"

Properties
ZCT	Coordinate `[get, set]`

ImageType	Type `[get, set]`

VolumeD	Volume `[get, set]`

string	Filename `[get, set]`

int	RGBChannelCount `[get]`

int?	MacroResolution `[get, set]`

int?	LabelResolution `[get, set]`

double	Resolution `[get, set]`

Statistics	Statistics `[get, set]`

string	ID `[get, set]`

int	ImageCount `[get]`

double	PhysicalSizeX `[get]`

double	PhysicalSizeY `[get]`

double	PhysicalSizeZ `[get]`

int	TileX `[get]`

int	TileY `[get]`

double	StageSizeX `[get, set]`

double	StageSizeY `[get, set]`

double	StageSizeZ `[get, set]`

Size	PyramidalSize `[get, set]`

PointD	PyramidalOrigin `[get, set]`

int	Level `[get, set]`

int	series `[get, set]`

Channel	RChannel `[get]`

Channel	GChannel `[get]`

Channel	BChannel `[get]`

int	SizeX `[get]`

int	SizeY `[get]`

int	SizeZ `[get]`

int	SizeC `[get]`

int	SizeT `[get]`

IntRange	RRange `[get]`

IntRange	GRange `[get]`

IntRange	BRange `[get]`

BufferInfo	SelectedBuffer `[get]`

bool	isRGB `[get]`

bool	isTime `[get]`

bool	isSeries `[get]`

bool	isPyramidal `[get]`

static bool	Initialized `[get]`

Detailed Description

Definition at line 5525 of file Bio.cs.

Member Enumeration Documentation

◆ ImageType

enum BioCore.BioImage.ImageType

Definition at line 5610 of file Bio.cs.

Constructor & Destructor Documentation

◆ BioImage()

BioCore.BioImage.BioImage ( string file )

Definition at line 7191 of file Bio.cs.

Member Function Documentation

◆ AutoThreshold() [1/2]

static void BioCore.BioImage.AutoThreshold ( )

static

It takes the current image, and the current image's statistics, and updates the image's statistics

Definition at line 11781 of file Bio.cs.

◆ AutoThreshold() [2/2]

static void BioCore.BioImage.AutoThreshold	(	BioImage	b,
		bool	updateImageStats
	)

static

It takes a BioImage object, and for each channel, it calculates the mean histogram of the channel, and then it calculates the mean histogram of the entire image

Parameters

BioImage	This is the image object that contains the image data.
updateImageStats	if true, the image stats will be updated.

Definition at line 11688 of file Bio.cs.

◆ AutoThresholdThread()

static void BioCore.BioImage.AutoThresholdThread ( BioImage b )

static

"This function creates a new thread and starts it, and the thread calls the AutoThreshold function."

The AutoThreshold function is the function that actually does the work.

Parameters

BioImage This is a class that contains the image data and some other information.

Definition at line 11791 of file Bio.cs.

◆ Bake() [1/2]

void BioCore.BioImage.Bake	(	int	rmin,
		int	rmax,
		int	gmin,
		int	gmax,
		int	bmin,
		int	bmax
	)

Bake(int rmin, int rmax, int gmin, int gmax, int bmin, int bmax)

Parameters

rmin	The minimum value of the red channel.
rmax	The maximum value of the red channel.
gmin	The minimum value of the green channel.
gmax	The maximum value of the green channel.
bmin	The minimum value of the blue channel.
bmax	The maximum value of the blue channel.

Definition at line 6758 of file Bio.cs.

◆ Bake() [2/2]

void BioCore.BioImage.Bake	(	IntRange	rf,
		IntRange	gf,
		IntRange	bf
	)

It takes a range of values for each channel, and creates a new image with the filtered values

Parameters

IntRange
IntRange
IntRange

Definition at line 6768 of file Bio.cs.

◆ Copy() [1/4]

BioImage BioCore.BioImage.Copy ( )

Definition at line 5777 of file Bio.cs.

◆ Copy() [2/4]

static BioImage BioCore.BioImage.Copy ( BioImage b )

static

Definition at line 5769 of file Bio.cs.

◆ Copy() [3/4]

static BioImage BioCore.BioImage.Copy	(	BioImage	b,
		bool	rois
	)

static

Definition at line 5736 of file Bio.cs.

◆ Copy() [4/4]

BioImage BioCore.BioImage.Copy ( bool rois )

Definition at line 5773 of file Bio.cs.

◆ CopyInfo()

static BioImage BioCore.BioImage.CopyInfo	(	BioImage	b,
		bool	copyAnnotations,
		bool	copyChannels
	)

static

Definition at line 5781 of file Bio.cs.

◆ Dispose()

void BioCore.BioImage.Dispose ( )

It disposes of all the buffers and channels in the image, removes the image from the Images list, and then calls the garbage collector

Definition at line 11799 of file Bio.cs.

◆ ExportROIFolder()

static void BioCore.BioImage.ExportROIFolder	(	string	path,
		string	filename
	)

static

ExportROIFolder(path, filename)

This function takes a folder path and a filename as input and exports all the ROIs in the folder as CSV files

Parameters

path	the path to the folder containing the OMERO ROI files
filename	the name of the file you want to export

Definition at line 11668 of file Bio.cs.

◆ ExportROIsCSV()

static void BioCore.BioImage.ExportROIsCSV	(	string	filename,
		List< ROI >	Annotations
	)

static

This function takes a list of ROIs and converts them to a string, then writes that string to a file

Parameters

filename	the name of the file to be saved
Annotations	List of ROI objects

Definition at line 11637 of file Bio.cs.

◆ ExtractRegionFromTiledTiff()

static BufferInfo BioCore.BioImage.ExtractRegionFromTiledTiff	(	BioImage	b,
		int	x,
		int	y,
		int	width,
		int	height,
		int	res
	)

static

Definition at line 10377 of file Bio.cs.

◆ FilesToStack()

static BioImage BioCore.BioImage.FilesToStack	(	string[]	files,
		int	sizeZ,
		int	sizeC,
		int	sizeT
	)

static

It takes a list of files, and creates a new BioImage object with the first file in the list, then adds the buffers from the rest of the files to the new BioImage object

Parameters

files	an array of file paths
sizeZ	number of images in the stack
sizeC	number of channels
sizeT	number of time points

Returns: A BioImage object.

Definition at line 9497 of file Bio.cs.

◆ FindFocus()

static int BioCore.BioImage.FindFocus	(	BioImage	im,
		int	Channel,
		int	Time
	)

static

Definition at line 10327 of file Bio.cs.

◆ FolderToStack()

static BioImage BioCore.BioImage.FolderToStack ( string path )

static

It takes a folder of images and creates a stack from them

Parameters

path	the path to the folder containing the images

Returns: A BioImage object.

Definition at line 9514 of file Bio.cs.

◆ GetAnnotations() [1/2]

List< ROI > BioCore.BioImage.GetAnnotations	(	int	Z,
		int	C,
		int	T
	)

This function returns a list of ROI objects that have the same Z, C, and T coordinates as the input parameters

Parameters

Z	The Z-plane of the image
C	Channel
T	Time

Returns: A list of ROI objects.

Definition at line 7934 of file Bio.cs.

◆ GetAnnotations() [2/2]

List< ROI > BioCore.BioImage.GetAnnotations ( ZCT coord )

‍GetAnnotations() returns a list of ROI objects that are associated with the ZCT coordinate

passed in as a parameter

Parameters

ZCT	a 3D coordinate (Z, C, T)

Returns: A list of ROI objects.

Definition at line 7914 of file Bio.cs.

◆ GetBitmap() [1/2]

Bitmap BioCore.BioImage.GetBitmap	(	int	z,
		int	c,
		int	t
	)

‍Get the bitmap from the buffer at the given coordinates

Parameters

z	the z-stack index
c	channel
t	time

Returns: A Bitmap object.

Definition at line 7590 of file Bio.cs.

◆ GetBitmap() [2/2]

Bitmap BioCore.BioImage.GetBitmap ( ZCT coord )

‍This function returns a Bitmap object from the image data stored in the OME-TIFF file

Parameters

ZCT	Z = Z-stack, C = channel, T = timepoint

Returns: A Bitmap object.

Definition at line 7780 of file Bio.cs.

◆ GetBitMaxValue()

static int BioCore.BioImage.GetBitMaxValue ( int bt )

static

It returns the maximum value of a bit.

Parameters

bt bit depth

Returns: The maximum value of a bit.

Definition at line 10620 of file Bio.cs.

◆ GetBitsPerPixel()

static int BioCore.BioImage.GetBitsPerPixel ( int bt )

static

‍If the number is less than or equal to 255, then it's 8 bits. If it's less than or equal

to 512, then it's 9 bits. If it's less than or equal to 1023, then it's 10 bits. If it's less than or equal to 2047, then it's 11 bits. If it's less than or equal to 4095, then it's 12 bits. If it's less than or equal to 8191, then it's 13 bits. If it's less than or equal to 16383, then it's 14 bits. If it's less than or equal to 32767, then it's 15 bits. If it's less than or equal to 65535, then it's 16 bits

Parameters

bt	The number of bits per pixel.

Returns: The number of bits per pixel.

Definition at line 10594 of file Bio.cs.

◆ GetChannelImage()

Bitmap BioCore.BioImage.GetChannelImage	(	int	ind,
		RGB	rGB
	)

It takes an image, and returns a single channel of that image

Parameters

ind	the index of the buffer
RGB	enum with R, G, B

Returns: A Bitmap

Definition at line 7831 of file Bio.cs.

◆ GetEmission()

Bitmap BioCore.BioImage.GetEmission	(	ZCT	coord,
		IntRange	rf,
		IntRange	gf,
		IntRange	bf
	)

It takes a ZCT coordinate and returns a bitmap of the emission image at that coordinate

Parameters

ZCT	Z, C, T coordinates
IntRange
IntRange
IntRange

Returns: A bitmap.

Definition at line 7855 of file Bio.cs.

◆ GetFiltered() [1/2]

Bitmap BioCore.BioImage.GetFiltered	(	int	ind,
		IntRange	r,
		IntRange	g,
		IntRange	b
	)

It takes a range of RGB values and returns a filtered image

Parameters

ind	the index of the buffer to get the filtered image from
IntRange
IntRange
IntRange

Returns: A Bitmap

Definition at line 7805 of file Bio.cs.

◆ GetFiltered() [2/2]

Bitmap BioCore.BioImage.GetFiltered	(	ZCT	coord,
		IntRange	r,
		IntRange	g,
		IntRange	b
	)

‍Get the image at the specified ZCT coordinate, and return a filtered version of it

Parameters

ZCT	Z is the Z-stack, C is the channel, T is the timepoint
IntRange
IntRange
IntRange

Returns: A bitmap.

Definition at line 7792 of file Bio.cs.

◆ GetImageByCoord()

Image BioCore.BioImage.GetImageByCoord	(	int	z,
		int	c,
		int	t
	)

It returns an image from a buffer based on the z, c, and t coordinates

Parameters

z	the z-stack index
c	channel
t	time

Returns: The image at the specified coordinates.

Definition at line 7579 of file Bio.cs.

◆ GetIndex()

int BioCore.BioImage.GetIndex	(	int	ix,
		int	iy
	)

Get index of pixel in the buffer.

Parameters

ix	x coordinate of the pixel
iy	The y coordinate of the pixel to get the index of.

Returns: The index of the pixel in the array.

Definition at line 7599 of file Bio.cs.

◆ GetIndexRGB()

int BioCore.BioImage.GetIndexRGB	(	int	ix,
		int	iy,
		int	index
	)

Get index of pixel in the buffer.

Parameters

ix	x coordinate of the pixel
iy	The y coordinate of the pixel
index	0 = Red, 1 = Green, 2 = Blue

Returns: The index of the pixel in the buffer.

Definition at line 7621 of file Bio.cs.

◆ GetLevelDownsample()

double BioCore.BioImage.GetLevelDownsample ( int level )

Get the downsampling factor of a given level.

Parameters

level The desired level.

<return> The downsampling factor for this level. </return>

Exceptions

OpenSlideException

Definition at line 5917 of file Bio.cs.

◆ GetPixelFormat() [1/2]

static PixelFormat BioCore.BioImage.GetPixelFormat	(	int	rgbChannelCount,
		int	bitsPerPixel
	)

static

If the bits per pixel is 8, then the pixel format is either 8bppIndexed, 24bppRgb, or 32bppArgb. If the bits per pixel is 16, then the pixel format is either 16bppGrayScale or 48bppRgb

Parameters

rgbChannelCount	The number of channels in the image. For example, a grayscale image has 1 channel, a color image has 3 channels (red, green, blue).
bitsPerPixel	8 or 16

Returns: The PixelFormat of the image.

Definition at line 10650 of file Bio.cs.

◆ GetPixelFormat() [2/2]

static PixelFormat BioCore.BioImage.GetPixelFormat	(	int	rgbChannelCount,
		ome.xml.model.enums.PixelType	px
	)

static

Definition at line 10670 of file Bio.cs.

◆ GetRGBBitmap()

Bitmap BioCore.BioImage.GetRGBBitmap	(	ZCT	coord,
		IntRange	rf,
		IntRange	gf,
		IntRange	bf
	)

‍Get the RGB bitmap for the specified ZCT coordinate

Parameters

ZCT	a 3-tuple of integers (z, c, t)
IntRange
IntRange
IntRange

Returns: A bitmap.

Definition at line 7881 of file Bio.cs.

◆ GetSeriesCount()

static int BioCore.BioImage.GetSeriesCount ( string file )

static

Definition at line 11047 of file Bio.cs.

◆ GetTile() [1/2]

static BufferInfo BioCore.BioImage.GetTile	(	BioImage	b,
		int	index,
		int	serie,
		int	tilex,
		int	tiley,
		int	tileSizeX,
		int	tileSizeY,
		bool	OpenSlide = `true`
	)

static

Definition at line 10482 of file Bio.cs.

◆ GetTile() [2/2]

static BufferInfo BioCore.BioImage.GetTile	(	BioImage	b,
		ZCT	coord,
		int	serie,
		int	tilex,
		int	tiley,
		int	tileSizeX,
		int	tileSizeY,
		bool	OpenSlide = `true`
	)

static

It reads a tile from a file, and returns a bitmap

Parameters

BioImage	This is a class that contains the image file name, the image reader, and the coordinates of the image.
ZCT	Z, C, T
serie	the series number (0-based).
tilex	the x coordinate of the tile.
tiley	the y coordinate of the tile.
tileSizeX	the width of the tile.
tileSizeY	the height of the tile.
OpenSlide	whether the tile should be opened with OpenSlide.

Returns: A Bitmap object.

Definition at line 10424 of file Bio.cs.

◆ GetTileRGB()

Bitmap BioCore.BioImage.GetTileRGB	(	ZCT	coord,
		int	serie,
		int	tilex,
		int	tiley,
		int	tileSizeX,
		int	tileSizeY
	)

Definition at line 10530 of file Bio.cs.

◆ GetUnitPerPixel()

double BioCore.BioImage.GetUnitPerPixel ( int level )

Get Unit Per Pixel for pyramidal images.

Parameters

level

Returns

Definition at line 5947 of file Bio.cs.

◆ GetValue() [1/3]

ushort BioCore.BioImage.GetValue	(	int	z,
		int	c,
		int	t,
		int	x,
		int	y
	)

‍This function returns the value of the pixel at the specified ZCTXY coordinates

Parameters

z	The Z-plane of the image.
c	channel
t	time
x	x coordinate of the pixel
y	the y coordinate of the pixel

Returns: The value of the pixel at the given coordinates.

Definition at line 7700 of file Bio.cs.

◆ GetValue() [2/3]

ushort BioCore.BioImage.GetValue	(	ZCT	coord,
		int	x,
		int	y
	)

‍Get the value of the pixel at the given coordinates

Parameters

ZCT	Z is the Z-plane, C is the channel, T is the timepoint
x	x coordinate of the pixel
y	The y coordinate of the pixel

Returns: The value of the pixel at the given coordinates.

Definition at line 7687 of file Bio.cs.

◆ GetValue() [3/3]

ushort BioCore.BioImage.GetValue ( ZCTXY coord )

‍This function returns the value of a pixel at a given coordinate

Parameters

ZCTXY a struct that contains the X, Y, Z, C, and T coordinates of the pixel.

Returns: The value of the pixel at the given coordinate.

Definition at line 7641 of file Bio.cs.

◆ GetValueRGB() [1/3]

ushort BioCore.BioImage.GetValueRGB	(	int	z,
		int	c,
		int	t,
		int	x,
		int	y,
		int	RGBindex
	)

This function returns the value of the pixel at the specified Z, C, T, X, Y, and RGBindex

Parameters

z	The Z-plane index
c	channel
t	time index
x	x coordinate of the pixel
y	The y coordinate of the pixel
RGBindex	0 = Red, 1 = Green, 2 = Blue

Returns: The value of the pixel at the given coordinates.

Definition at line 7732 of file Bio.cs.

◆ GetValueRGB() [2/3]

ushort BioCore.BioImage.GetValueRGB	(	ZCT	coord,
		int	x,
		int	y,
		int	RGBindex
	)

‍Get the value of a pixel at a given coordinate

Parameters

ZCT	The ZCT coordinate of the image.
x	x coordinate of the pixel
y	the y coordinate of the pixel
RGBindex	0 = Red, 1 = Green, 2 = Blue

Returns: The value of the pixel at the given coordinates.

Definition at line 7712 of file Bio.cs.

◆ GetValueRGB() [3/3]

ushort BioCore.BioImage.GetValueRGB	(	ZCTXY	coord,
		int	index
	)

‍Get the value of the pixel at the given coordinates in the given buffer

Parameters

ZCTXY	a struct that contains the Z, C, T, X, and Y coordinates of the pixel.
index	0, 1, 2

Returns: A ushort value.

Definition at line 7666 of file Bio.cs.

◆ ImagesToStack()

static BioImage BioCore.BioImage.ImagesToStack ( string[] files )

static

It takes a list of files, opens them, and stacks them into a single BioImage object

Parameters

files an array of file paths

Returns: A BioImage object.

Definition at line 10906 of file Bio.cs.

◆ ImportROIsCSV()

static List< ROI > BioCore.BioImage.ImportROIsCSV ( string filename )

static

It reads the CSV file and converts each line into a ROI object

Parameters

filename The path to the CSV file.

Returns: A list of ROI objects.

Definition at line 11648 of file Bio.cs.

◆ Initialize()

static void BioCore.BioImage.Initialize ( )

static

We initialize OME on a seperate thread so the user doesn't have to wait for initialization to view images.

Definition at line 7948 of file Bio.cs.

◆ isOME()

static bool BioCore.BioImage.isOME ( string file )

static

If the file is a TIFF, check the image description for the OME XML. If it's not a TIFF, assume it's OME

Parameters

file	the file path of the image

Returns: A boolean value.

Definition at line 8557 of file Bio.cs.

◆ isOMESeries()

static bool BioCore.BioImage.isOMESeries ( string file )

static

‍If the file is an OME file and has more than one series, then it is a series

Parameters

file	the file path to the image

Returns: A boolean value.

Definition at line 8584 of file Bio.cs.

◆ isTiffSeries()

static bool BioCore.BioImage.isTiffSeries ( string file )

static

‍The function checks if the image is a tiff image and if it is, it checks if the image is a

series of images

Parameters

file	the path to the file

Returns: a boolean value.

Definition at line 8523 of file Bio.cs.

◆ LevelFromResolution()

int BioCore.BioImage.LevelFromResolution ( double Resolution )

Returns the level of a given resolution.

Parameters

Resolution

Returns

Definition at line 5928 of file Bio.cs.

◆ MergeChannels() [1/2]

static BioImage BioCore.BioImage.MergeChannels	(	BioImage	b2,
		BioImage	b
	)

static

This function takes two images and merges them together

Parameters

BioImage	The image to be merged
BioImage	The image to be merged

Returns: A new BioImage object.

Definition at line 7262 of file Bio.cs.

◆ MergeChannels() [2/2]

static BioImage BioCore.BioImage.MergeChannels	(	string	bname,
		string	b2name
	)

static

MergeChannels(b, b2) takes two images, b and b2, and merges the channels of b2 into b

Parameters

bname	The name of the first image
b2name	The name of the image to be merged with the first image.

Returns: A BioImage object.

Definition at line 7353 of file Bio.cs.

◆ MergeT()

static BioImage BioCore.BioImage.MergeT ( BioImage b )

static

It takes a 3D image and merges the time dimension into a single image.

Parameters

BioImage The image to be processed

Returns: A new BioImage object.

Definition at line 7407 of file Bio.cs.

◆ MergeZ()

static BioImage BioCore.BioImage.MergeZ ( BioImage b )

static

It takes a 3D image and merges the Z-stack into a single 2D image

Parameters

BioImage The image to be merged

Returns: A new BioImage object.

Definition at line 7364 of file Bio.cs.

◆ Open() [1/2]

static void BioCore.BioImage.Open ( string file )

static

It opens a file

Parameters

file	The file to open.

Definition at line 10873 of file Bio.cs.

◆ Open() [2/2]

static void BioCore.BioImage.Open ( string[] files )

static

It opens a file

Parameters

files The files to open.

Definition at line 10880 of file Bio.cs.

◆ OpenAsync() [1/2]

static async Task BioCore.BioImage.OpenAsync	(	string	file,
		bool	OME,
		bool	newtab,
		bool	images,
		int	series
	)

static

It opens a file in a new thread.

Parameters

file	The file to open

Definition at line 10726 of file Bio.cs.

◆ OpenAsync() [2/2]

static async Task BioCore.BioImage.OpenAsync	(	string[]	files,
		bool	OME,
		bool	tab,
		bool	images
	)

static

It opens a file asynchronously

Parameters

files The file(s) to open.

Definition at line 10738 of file Bio.cs.

◆ OpenFile() [1/4]

static BioImage BioCore.BioImage.OpenFile ( string file )

static

This function opens a file and returns a BioImage object

Parameters

file	The path to the file you want to open.

Returns: A BioImage object.

Definition at line 8121 of file Bio.cs.

◆ OpenFile() [2/4]

static BioImage BioCore.BioImage.OpenFile	(	string	file,
		int	series,
		bool	newTab
	)

static

It opens a file, reads the metadata, reads the image data, and then calculates the image statistics

Parameters

file	The file to open
series	The series number of the image to open.

Returns: A BioImage object

Definition at line 8220 of file Bio.cs.

◆ OpenFile() [3/4]

static BioImage BioCore.BioImage.OpenFile	(	string	file,
		int	series,
		bool	newTab,
		bool	addToImages,
		bool	tile,
		int	x,
		int	y,
		int	w,
		int	h
	)

static

It opens a file, reads the metadata, reads the image data, and then calculates the image statistics

Parameters

file	The file to open
series	The series number of the image to open.

Returns: A BioImage object

Definition at line 8231 of file Bio.cs.

◆ OpenFile() [4/4]

static BioImage BioCore.BioImage.OpenFile	(	string	file,
		int	series,
		bool	tab,
		bool	addToImages
	)

static

It opens a TIFF file and returns a BioImage object

Parameters

file	the file path
series	the series number of the image to open

Returns: A BioImage object.

Definition at line 10752 of file Bio.cs.

◆ OpenOME() [1/3]

static BioImage BioCore.BioImage.OpenOME ( string file )

static

‍This function opens an OME file and returns a BioImage object

Parameters

file	the path to the file you want to open

Returns: A list of BioImages.

Definition at line 9471 of file Bio.cs.

◆ OpenOME() [2/3]

static BioImage BioCore.BioImage.OpenOME	(	string	file,
		int	serie,
		bool	newTab,
		bool	addToImages
	)

static

‍OpenOME(string file, int serie)

The first parameter is a string, the second is an integer

Parameters

file	the path to the file
serie	the image series to open

Returns: A BioImage object.

Definition at line 9483 of file Bio.cs.

◆ OpenOME() [3/3]

static BioImage BioCore.BioImage.OpenOME	(	string	file,
		int	serie,
		bool	tab,
		bool	addToImages,
		bool	tile,
		int	tilex,
		int	tiley,
		int	tileSizeX,
		int	tileSizeY,
		bool	useOpenSlide = `true`
	)

static

Definition at line 9547 of file Bio.cs.

◆ OpenOMEROIs()

static List< ROI > BioCore.BioImage.OpenOMEROIs	(	string	file,
		int	series
	)

static

This function takes a file path to an OME-TIFF file and returns a list of ROI objects

Parameters

file	the path to the OME-TIFF file
series	the series number of the image you want to open

Returns: A list of ROI objects.

Definition at line 11090 of file Bio.cs.

◆ OpenOMESeries()

static BioImage[] BioCore.BioImage.OpenOMESeries	(	string	file,
		bool	newTab,
		bool	addToImages
	)

static

It opens an OME-TIFF file, and returns an array of BioImage objects, one for each series in the file

Parameters

file	the path to the file

Returns: An array of BioImage objects.

Definition at line 10694 of file Bio.cs.

◆ OpenSeries()

static BioImage[] BioCore.BioImage.OpenSeries ( string file )

static

It opens a tiff file, reads the number of pages, reads the number of channels, and then reads each page into a BioImage object

Parameters

file	the path to the file

Returns: An array of BioImage objects.

Definition at line 8089 of file Bio.cs.

◆ OpenVip()

static void BioCore.BioImage.OpenVip	(	BioImage	b,
		int	pagenumber,
		int	x,
		int	y,
		int	w,
		int	h
	)

static

Definition at line 6820 of file Bio.cs.

◆ OpenVips()

static void BioCore.BioImage.OpenVips	(	BioImage	b,
		int	pagecount
	)

static

Definition at line 6805 of file Bio.cs.

◆ OpenXML()

static string BioCore.BioImage.OpenXML ( string file )

static

‍Open the file, get the image description field, and return it as a string

Parameters

file	the path to the file

Returns: The image description of the tiff file.

Definition at line 11075 of file Bio.cs.

◆ operator*() [1/2]

static BioImage BioCore.BioImage.operator*	(	BioImage	a,
		ColorS	b
	)

static

It takes a BioImage and a ColorS and returns a BioImage

Parameters

BioImage	a class that contains a list of ColorS objects.
ColorS	a struct that contains a byte for each color channel (R, G, B, A)

Returns: A BioImage object.

Definition at line 11898 of file Bio.cs.

◆ operator*() [2/2]

static BioImage BioCore.BioImage.operator*	(	BioImage	a,
		float	b
	)

static

This function multiplies each pixel in the image by a constant value

Parameters

BioImage	a class that contains a list of buffers (which are 2D arrays of floats)
b	the image to be multiplied

Returns: The image itself.

Definition at line 11841 of file Bio.cs.

◆ operator+() [1/2]

static BioImage BioCore.BioImage.operator+	(	BioImage	a,
		ColorS	b
	)

static

It takes a BioImage object and a ColorS object and adds the ColorS object to each of the buffers in the BioImage object

Parameters

BioImage	a class that contains a list of ColorS objects.
ColorS	a struct that contains a byte for each color channel (R, G, B, A)

Returns: A BioImage object

Definition at line 11913 of file Bio.cs.

◆ operator+() [2/2]

static BioImage BioCore.BioImage.operator+	(	BioImage	a,
		float	b
	)

static

This function adds a constant value to each pixel in the image

Parameters

BioImage	a class that contains a list of buffers (float[])
b	the value to add to the image

Returns: The image itself.

Definition at line 11855 of file Bio.cs.

◆ operator-() [1/2]

static BioImage BioCore.BioImage.operator-	(	BioImage	a,
		ColorS	b
	)

static

The function subtracts a color from each pixel in the image

Parameters

BioImage	a class that contains a list of ColorS objects.
ColorS	a struct that contains a byte for each color channel (R, G, B, A)

Returns: The image is being returned.

Definition at line 11927 of file Bio.cs.

◆ operator-() [2/2]

static BioImage BioCore.BioImage.operator-	(	BioImage	a,
		float	b
	)

static

This function subtracts a float from each pixel in the image

Parameters

BioImage	a class that contains a list of buffers (which are 2D arrays of floats)
b	the value to subtract from the image

Returns: The image is being returned.

Definition at line 11869 of file Bio.cs.

◆ operator/() [1/2]

static BioImage BioCore.BioImage.operator/	(	BioImage	a,
		ColorS	b
	)

static

This function divides the color of each pixel in the image by the color of the second image

Parameters

BioImage	a class that contains a list of ColorS objects.
ColorS	a struct that contains a byte for each color channel (R, G, B, A)

Returns: A BioImage object.

Definition at line 11884 of file Bio.cs.

◆ operator/() [2/2]

static BioImage BioCore.BioImage.operator/	(	BioImage	a,
		float	b
	)

static

This function divides each pixel in the image by a constant value

Parameters

BioImage	a class that contains a list of buffers (which are 2D arrays of floats)
b	the value to divide by

Returns: The image itself.

Definition at line 11827 of file Bio.cs.

◆ ROIsToString()

static string BioCore.BioImage.ROIsToString ( List< ROI > Annotations )

static

It takes a list of ROI objects and returns a string of all the ROI objects in the list

Parameters

Annotations List of ROI objects

Returns: A string of the ROI's in the list.

Definition at line 11431 of file Bio.cs.

◆ ROIToString()

static string BioCore.BioImage.ROIToString ( ROI an )

static

This function takes an ROI object and converts it to a string that can be written to a file

Parameters

ROI	The ROI object

Returns: A string

Definition at line 11445 of file Bio.cs.

◆ RotateFlip()

void BioCore.BioImage.RotateFlip ( RotateFlipType rot )

It rotates and flips the image

Parameters

RotateFlipType

Definition at line 6743 of file Bio.cs.

◆ Save()

static void BioCore.BioImage.Save	(	string	file,
		string	ID
	)

static

It takes a file and an ID and saves the file to the ID

Parameters

file	The file to save the data to.
ID	The ID of the user

Definition at line 10891 of file Bio.cs.

◆ SaveAsync()

static async Task BioCore.BioImage.SaveAsync	(	string	file,
		string	id,
		int	serie,
		bool	ome
	)

static

The SaveAsync function saves data to a file asynchronously.

Parameters

file	The file parameter is a string that represents the file path or name where the data will be saved.
id	The "id" parameter is a string that represents an identifier for the save operation. It could be used to uniquely identify the saved data or to specify a specific location or format for the saved file.
serie	The "serie" parameter is an integer that represents a series or sequence number. It is used as a parameter in the SaveAsync method.
ome	The "ome" parameter is a boolean value that determines whether or not to perform a specific action in the saving process.

Definition at line 10786 of file Bio.cs.

◆ SaveFile()

static void BioCore.BioImage.SaveFile	(	string	file,
		string	ID
	)

static

This function takes a string array of file names and a string ID and saves the files to the database

Parameters

file	The file path of the file to be saved.
ID	The ID of the series you want to save.

Definition at line 7969 of file Bio.cs.

◆ SaveOME()

static void BioCore.BioImage.SaveOME	(	string	file,
		string	ID
	)

static

This function takes a string array of IDs and a file name and saves the OME-TIFF file

Parameters

file	the file to save to
ID	The ID of the image to be saved

Definition at line 8604 of file Bio.cs.

◆ SaveOMEPyramidal()

static void BioCore.BioImage.SaveOMEPyramidal	(	BioImage[]	bms,
		string	file,
		Enums.ForeignTiffCompression	compression,
		int	compressionLevel
	)

static

The function SaveOMEPyramidal saves a collection of BioImages as a pyramidal OME-TIFF file.

Parameters

bms	An array of BioImage objects representing the images to be saved.
file	The `file` parameter is a string that represents the file path where the OME Pyramidal TIFF file will be saved.
compression	The `compression` parameter is of type `Enums.ForeignTiffCompression` and it specifies the compression method to be used when saving the TIFF file.

Definition at line 9330 of file Bio.cs.

◆ SaveOMESeries() [1/2]

static void BioCore.BioImage.SaveOMESeries	(	BioImage[]	bms,
		string	f,
		bool	planes
	)

static

Definition at line 8943 of file Bio.cs.

◆ SaveOMESeries() [2/2]

static void BioCore.BioImage.SaveOMESeries	(	string[]	files,
		string	f,
		bool	planes
	)

static

It saves a series of images to a file, and adds OME-XML metadata to the file

Parameters

files	an array of file paths to the images to be saved
f	the file name to save to
planes	if true, the planes will be saved as well.

Definition at line 8615 of file Bio.cs.

◆ SaveOMEStiched()

static void BioCore.BioImage.SaveOMEStiched	(	BioImage[]	bms,
		string	file,
		string	compression
	)

static

Definition at line 8952 of file Bio.cs.

◆ SavePyramidalAsync()

static async Task BioCore.BioImage.SavePyramidalAsync	(	BioImage[]	imgs,
		string	file,
		Enums.ForeignTiffCompression	com,
		int	compLevel
	)

static

The function SavePyramidalAsync saves an array of BioImage objects as a pyramidal TIFF file asynchronously.

Parameters

imgs	imgs is an array of BioImage objects.
file	The "file" parameter is a string that represents the file path where the pyramidal image will be saved.
com	The parameter "com" is of type Enums.ForeignTiffCompression, which is an enumeration representing different compression options for the TIFF file.
compLevel	The `compLevel` parameter is an integer that represents the compression level for the TIFF file. It is used to specify the level of compression to be applied to the image data when saving the pyramidal image. The higher the compression level, the smaller the file size but potentially lower image quality.

Definition at line 10850 of file Bio.cs.

◆ SaveSeries()

static void BioCore.BioImage.SaveSeries	(	string[]	files,
		string	ID
	)

static

It takes a list of image files, and saves them as a multi-page TIFF file

Parameters

files	An array of file paths to the images to be saved.
ID	The file name of the output file.

Definition at line 7979 of file Bio.cs.

◆ SaveSeriesAsync()

static async Task BioCore.BioImage.SaveSeriesAsync	(	BioImage[]	imgs,
		string	file,
		bool	ome
	)

static

The function SaveSeriesAsync saves a series of BioImage objects to a file asynchronously.

Parameters

imgs	imgs is an array of BioImage objects.
file	The "file" parameter is a string that represents the file path where the series of BioImages will be saved.
ome	The "ome" parameter is a boolean flag that indicates whether the images should be saved in OME-TIFF format or not. If "ome" is set to true, the images will be saved in OME-TIFF format. If "ome" is set to false, the images will be

Definition at line 10819 of file Bio.cs.

◆ SetValue() [1/3]

void BioCore.BioImage.SetValue	(	int	x,
		int	y,
		int	ind,
		ushort	value
	)

It sets the value of a pixel in a buffer

Parameters

x	The x coordinate of the pixel to set.
y	The y coordinate of the pixel to set.
ind	The index of the buffer to set the value in.
value	The value to set the pixel to.

Definition at line 7751 of file Bio.cs.

◆ SetValue() [2/3]

void BioCore.BioImage.SetValue	(	int	x,
		int	y,
		ZCT	coord,
		ushort	value
	)

This function sets the value of a pixel at a given x,y coordinate in a given image plane

Parameters

x	x coordinate of the pixel
y	The y coordinate of the pixel to set.
ZCT	a struct that contains the Z, C, and T coordinates of the pixel
value	the value to set

Definition at line 7761 of file Bio.cs.

◆ SetValue() [3/3]

void BioCore.BioImage.SetValue	(	ZCTXY	coord,
		ushort	value
	)

It takes a coordinate and a value, and sets the value at that coordinate

Parameters

ZCTXY	a struct that contains the Z, C, T, X, and Y coordinates of the pixel.
value	The value to set the pixel to.

Definition at line 7740 of file Bio.cs.

◆ SetValueRGB()

void BioCore.BioImage.SetValueRGB	(	ZCTXY	coord,
		int	RGBindex,
		ushort	value
	)

It takes a coordinate and a value and sets the value at that coordinate in the buffer

Parameters

ZCTXY	a struct that contains the Z, C, T, X, and Y coordinates of the pixel
RGBindex	0 = Red, 1 = Green, 2 = Blue
value	the value to be set

Definition at line 7770 of file Bio.cs.

◆ SplitChannels() [1/3]

BioImage[] BioCore.BioImage.SplitChannels ( )

It takes a single image and splits it into three separate images, one for each color channel

Returns: An array of BioImages.

Definition at line 7448 of file Bio.cs.

◆ SplitChannels() [2/3]

static BioImage[] BioCore.BioImage.SplitChannels ( BioImage bb )

static

‍SplitChannels splits a BioImage into its constituent channels

Parameters

BioImage The image to split

Returns: An array of BioImages

Definition at line 7552 of file Bio.cs.

◆ SplitChannels() [3/3]

static BioImage[] BioCore.BioImage.SplitChannels ( string name )

static

This function takes an image and splits it into its individual channels

Parameters

name	The name of the image to split.

Returns: An array of BioImage objects.

Definition at line 7561 of file Bio.cs.

◆ StackThreshold()

void BioCore.BioImage.StackThreshold ( bool bit16 )

This function sets the minimum and maximum values of the image to the minimum and maximum values of the stack

Parameters

bit16 true = 16 bit, false = 8 bit

Definition at line 10555 of file Bio.cs.

◆ StringToROI()

static ROI BioCore.BioImage.StringToROI ( string sts )

static

It takes a string of comma separated values and returns an ROI object

Parameters

sts	the string that contains the ROI data

Returns: A ROI object.

Definition at line 11470 of file Bio.cs.

◆ Substack()

static BioImage BioCore.BioImage.Substack	(	BioImage	orig,
		int	ser,
		int	zs,
		int	ze,
		int	cs,
		int	ce,
		int	ts,
		int	te
	)

static

It takes a BioImage object, and returns a new BioImage object that is a subset of the original

Parameters

BioImage	the image to be processed
ser	series number
zs	starting z-plane
ze	end of z-stack
cs	channel start
ce	channel end
ts	time start
te	time end

Returns: A new BioImage object.

Definition at line 7213 of file Bio.cs.

◆ To16Bit()

void BioCore.BioImage.To16Bit ( )

It converts the image to 16 bit, and then calculates the threshold for the image

Returns: A list of BufferInfo objects.

Definition at line 6363 of file Bio.cs.

◆ To24Bit()

void BioCore.BioImage.To24Bit ( )

Converts a 16 bit image to a 24 bit image

Returns: A Bitmap

Definition at line 6473 of file Bio.cs.

◆ To32Bit()

void BioCore.BioImage.To32Bit ( )

It converts the image to 32 bit format

Returns: A Bitmap object

Definition at line 6598 of file Bio.cs.

◆ To48Bit()

void BioCore.BioImage.To48Bit ( )

It converts the image to 48 bit RGB

Returns: A list of BufferInfo objects.

Definition at line 6627 of file Bio.cs.

◆ To8Bit()

void BioCore.BioImage.To8Bit ( )

It converts a 16-bit image to an 8-bit image

Returns: A list of BufferInfo objects.

Definition at line 6265 of file Bio.cs.

◆ ToImageSizeX()

double BioCore.BioImage.ToImageSizeX ( double d )

Convert a physical distance to an image distance

Parameters

d	the distance in millimeters

Returns: The value of d divided by the physicalSizeX.

Definition at line 6975 of file Bio.cs.

◆ ToImageSizeY()

double BioCore.BioImage.ToImageSizeY ( double d )

Convert a physical distance to an image distance

Parameters

d	the distance in millimeters

Returns: The image size in the Y direction.

Definition at line 6987 of file Bio.cs.

◆ ToImageSpace() [1/4]

PointD[] BioCore.BioImage.ToImageSpace ( List< PointD > p )

It takes a list of points in physical space and returns a list of points in image space

Parameters

p	List of points in stage space

Returns: A PointD array.

Definition at line 7034 of file Bio.cs.

◆ ToImageSpace() [2/4]

PointD BioCore.BioImage.ToImageSpace ( PointD p )

‍The function takes a point in the stage coordinate system and returns a point in the image

coordinate system

Parameters

PointD a class that contains two double values, X and Y.

Returns: A PointD object.

Definition at line 7024 of file Bio.cs.

◆ ToImageSpace() [3/4]

PointF[] BioCore.BioImage.ToImageSpace ( PointF[] p )

‍The function takes a list of points in the stage coordinate system and returns a list of

points in the image coordinate system

Parameters

p	the points to be converted

Returns: A PointF array.

Definition at line 7049 of file Bio.cs.

◆ ToImageSpace() [4/4]

System.Drawing.RectangleF BioCore.BioImage.ToImageSpace ( RectangleD p )

‍Convert a rectangle in physical space to a rectangle in image space

Parameters

RectangleD

Returns: A RectangleF object.

Definition at line 7064 of file Bio.cs.

◆ ToImageSpaceX()

double BioCore.BioImage.ToImageSpaceX ( double x )

‍Convert a stage coordinate to an image coordinate

Parameters

x	the x coordinate of the point in the image

Returns: The return value is a double.

Definition at line 6999 of file Bio.cs.

◆ ToImageSpaceY()

double BioCore.BioImage.ToImageSpaceY ( double y )

‍Convert a Y coordinate from stage space to image space

Parameters

y	the y coordinate of the point in the image

Returns: The return value is the y-coordinate of the image.

Definition at line 7011 of file Bio.cs.

◆ ToStageSpace() [1/7]

PointD BioCore.BioImage.ToStageSpace ( PointD p )

‍The function takes a point in the volume space and returns a point in the stage space

Parameters

PointD A struct that contains an X and Y value.

Returns: A PointD object.

Definition at line 7079 of file Bio.cs.

◆ ToStageSpace() [2/7]

static PointD BioCore.BioImage.ToStageSpace	(	PointD	p,
		double	physicalSizeX,
		double	physicalSizeY,
		double	volumeX,
		double	volumeY
	)

static

‍The function takes a point in the volume space and converts it to a point in the stage

space

Parameters

PointD	A custom class that holds an X and Y coordinate.
physicalSizeX	The width of the stage in mm
physicalSizeY	The height of the stage in mm
volumeX	The X coordinate of the top left corner of the volume in stage space.
volumeY	The Y position of the top left corner of the volume in stage space.

Returns: A PointD object.

Definition at line 7096 of file Bio.cs.

◆ ToStageSpace() [3/7]

PointD BioCore.BioImage.ToStageSpace	(	PointD	p,
		int	resolution
	)

Convert a point in the image space to a point in the stage space

Parameters

PointD	A point in the image space
resolution	the resolution of the image (0, 1, 2, 3, 4)

Returns: A PointD object.

Definition at line 7184 of file Bio.cs.

◆ ToStageSpace() [4/7]

PointD[] BioCore.BioImage.ToStageSpace ( PointD[] p )

‍It takes a list of points in the coordinate system of the image and returns a list of

points in the coordinate system of the stage

Parameters

p	The array of points to convert

Returns: A PointD[] array.

Definition at line 7143 of file Bio.cs.

◆ ToStageSpace() [5/7]

static PointD[] BioCore.BioImage.ToStageSpace	(	PointD[]	p,
		double	physicalSizeX,
		double	physicalSizeY,
		double	volumeX,
		double	volumeY
	)

static

It takes a list of points, and converts them from a coordinate system where the origin is in the center of the image, to a coordinate system where the origin is in the top left corner of the image

Parameters

p	the array of points to convert
physicalSizeX	The width of the image in microns
physicalSizeY	The height of the image in microns
volumeX	The X position of the volume in stage space.
volumeY	The Y position of the top left corner of the volume in stage space.

Returns: A PointD array.

Definition at line 7166 of file Bio.cs.

◆ ToStageSpace() [6/7]

RectangleD BioCore.BioImage.ToStageSpace ( RectangleD p )

‍Convert a rectangle from the coordinate space of the image to the coordinate space of the

stage

Parameters

RectangleD A rectangle with double precision coordinates.

Returns: A RectangleD object.

Definition at line 7109 of file Bio.cs.

◆ ToStageSpace() [7/7]

static RectangleD BioCore.BioImage.ToStageSpace	(	RectangleD	p,
		double	physicalSizeX,
		double	physicalSizeY,
		double	volumeX,
		double	volumeY
	)

static

‍This function takes a rectangle in the coordinate space of the image and converts it to the

coordinate space of the stage

Parameters

RectangleD	A rectangle with double precision.
physicalSizeX	The width of the stage in pixels
physicalSizeY	The height of the stage in pixels
volumeX	The X position of the volume in stage space.
volumeY	The Y position of the top of the volume in stage space.

Returns: A RectangleD object.

Definition at line 7128 of file Bio.cs.

◆ ToString()

override string BioCore.BioImage.ToString ( )

This function returns a string that contains the filename of the object, and the location of the object

Returns: The filename, and the location of the volume.

Definition at line 11816 of file Bio.cs.

◆ Update() [1/2]

void BioCore.BioImage.Update ( )

It updates the current object.

Definition at line 10949 of file Bio.cs.

◆ Update() [2/2]

static void BioCore.BioImage.Update ( BioImage b )

static

The function takes a BioImage object, opens the file, and returns a new BioImage object

Parameters

BioImage This is the class that contains the image data.

Definition at line 10944 of file Bio.cs.

◆ UpdateBuffersPyramidal()

async void BioCore.BioImage.UpdateBuffersPyramidal ( )

Updates the Buffers based on current pyramidal origin and resolution.

Definition at line 5954 of file Bio.cs.

◆ UpdateCoords() [1/3]

void BioCore.BioImage.UpdateCoords ( )

Definition at line 6836 of file Bio.cs.

◆ UpdateCoords() [2/3]

void BioCore.BioImage.UpdateCoords	(	int	sz,
		int	sc,
		int	st
	)

It takes the number of Z, C, and T planes in the image and then assigns each image buffer a coordinate in the ZCT space

Parameters

sz	number of z-slices
sc	number of channels
st	number of time points

Definition at line 6871 of file Bio.cs.

◆ UpdateCoords() [3/3]

void BioCore.BioImage.UpdateCoords	(	int	sz,
		int	sc,
		int	st,
		string	order
	)

It takes a list of images and assigns them to a 3D array of coordinates

Parameters

sz	size of the Z dimension
sc	number of channels
st	number of time points
order	XYCZT or XYZCT

Definition at line 6909 of file Bio.cs.

◆ VipsSupport()

static bool BioCore.BioImage.VipsSupport ( string file )

static

Definition at line 10535 of file Bio.cs.

Member Data Documentation

◆ Annotations

List<ROI> BioCore.BioImage.Annotations = new List<ROI>()

Definition at line 5631 of file Bio.cs.

◆ bitsPerPixel

int BioCore.BioImage.bitsPerPixel

Definition at line 5692 of file Bio.cs.

◆ Buffers

List<BufferInfo> BioCore.BioImage.Buffers = new List<BufferInfo>()

Definition at line 5629 of file Bio.cs.

◆ Channels

List<Channel> BioCore.BioImage.Channels = new List<Channel>()

Definition at line 5627 of file Bio.cs.

◆ columns

const string BioCore.BioImage.columns = "ROIID,ROINAME,TYPE,ID,SHAPEINDEX,TEXT,S,C,Z,T,X,Y,W,H,POINTS,STROKECOLOR,STROKECOLORW,FILLCOLOR,FONTSIZE\n"

static

Definition at line 11068 of file Bio.cs.

◆ Coords

int [,,] BioCore.BioImage.Coords

Definition at line 5596 of file Bio.cs.

◆ file

string BioCore.BioImage.file

Definition at line 6253 of file Bio.cs.

◆ filename

string BioCore.BioImage.filename = ""

Definition at line 5636 of file Bio.cs.

◆ filter16

LevelsLinear16bpp BioCore.BioImage.filter16 = new LevelsLinear16bpp()

static

Definition at line 7567 of file Bio.cs.

◆ filter8

LevelsLinear BioCore.BioImage.filter8 = new LevelsLinear()

static

Definition at line 7566 of file Bio.cs.

◆ frameInterval

double BioCore.BioImage.frameInterval = 0

Definition at line 5695 of file Bio.cs.

◆ imagesPerSeries

int BioCore.BioImage.imagesPerSeries = 0

Definition at line 5693 of file Bio.cs.

◆ imRead

ImageReader BioCore.BioImage.imRead = null

Definition at line 10324 of file Bio.cs.

◆ isGroup

bool BioCore.BioImage.isGroup = false

Definition at line 5697 of file Bio.cs.

◆ littleEndian

bool BioCore.BioImage.littleEndian = false

Definition at line 5696 of file Bio.cs.

◆ Loading

bool BioCore.BioImage.Loading = false

Definition at line 7945 of file Bio.cs.

◆ loadTimeMS

long BioCore.BioImage.loadTimeMS = 0

Definition at line 5698 of file Bio.cs.

◆ loadTimeTicks

long BioCore.BioImage.loadTimeTicks = 0

Definition at line 5699 of file Bio.cs.

◆ NewLine

const char BioCore.BioImage.NewLine = '\n'

static

Definition at line 11067 of file Bio.cs.

◆ openSlideBase

OpenSlideBase BioCore.BioImage.openSlideBase

Definition at line 5633 of file Bio.cs.

◆ openSlideImage

OpenSlideImage BioCore.BioImage.openSlideImage

Definition at line 5632 of file Bio.cs.

◆ Planes

bool BioCore.BioImage.Planes = false

static

Definition at line 6042 of file Bio.cs.

◆ Plate

WellPlate BioCore.BioImage.Plate = null

Definition at line 5618 of file Bio.cs.

◆ Resolutions

List<Resolution> BioCore.BioImage.Resolutions = new List<Resolution>()

Definition at line 5628 of file Bio.cs.

◆ rgbChannels

int [] BioCore.BioImage.rgbChannels = new int[3]

Definition at line 5649 of file Bio.cs.

◆ script

string BioCore.BioImage.script = ""

Definition at line 5637 of file Bio.cs.

◆ selected

bool BioCore.BioImage.selected = false

Definition at line 5700 of file Bio.cs.

◆ seriesCount

int BioCore.BioImage.seriesCount = 1

Definition at line 5694 of file Bio.cs.

◆ slideBase

SlideBase BioCore.BioImage.slideBase

Definition at line 5634 of file Bio.cs.

◆ slideImage

SlideImage BioCore.BioImage.slideImage

Definition at line 5635 of file Bio.cs.

◆ swatch

Stopwatch BioCore.BioImage.swatch = new Stopwatch()

static

Definition at line 7907 of file Bio.cs.

◆ vipPages

get

Definition at line 5842 of file Bio.cs.

◆ Type

ImageType BioCore.BioImage.Type

getset

Definition at line 5619 of file Bio.cs.

◆ Volume

VolumeD BioCore.BioImage.Volume

getset

Definition at line 5630 of file Bio.cs.

The documentation for this class was generated from the following file:

BioCore/BioCore/Source/Bio.cs

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Properties

Detailed Description

Member Enumeration Documentation

◆ ImageType

Constructor & Destructor Documentation

◆ BioImage()

Member Function Documentation

◆ AutoThreshold() [1/2]

◆ AutoThreshold() [2/2]

◆ AutoThresholdThread()

◆ Bake() [1/2]

◆ Bake() [2/2]

◆ Copy() [1/4]

◆ Copy() [2/4]

◆ Copy() [3/4]

◆ Copy() [4/4]

◆ CopyInfo()

◆ Dispose()

◆ ExportROIFolder()

◆ ExportROIsCSV()

◆ ExtractRegionFromTiledTiff()

◆ FilesToStack()

◆ FindFocus()

◆ FolderToStack()

◆ GetAnnotations() [1/2]

◆ GetAnnotations() [2/2]

◆ GetBitmap() [1/2]

◆ GetBitmap() [2/2]

◆ GetBitMaxValue()

◆ GetBitsPerPixel()

◆ GetChannelImage()

◆ GetEmission()

◆ GetFiltered() [1/2]

◆ GetFiltered() [2/2]

◆ GetImageByCoord()

◆ GetIndex()

◆ GetIndexRGB()

◆ GetLevelDownsample()

◆ GetPixelFormat() [1/2]

◆ GetPixelFormat() [2/2]

◆ GetRGBBitmap()

◆ GetSeriesCount()

◆ GetTile() [1/2]

◆ GetTile() [2/2]

◆ GetTileRGB()

◆ GetUnitPerPixel()

◆ GetValue() [1/3]

◆ GetValue() [2/3]

◆ GetValue() [3/3]

◆ GetValueRGB() [1/3]

◆ GetValueRGB() [2/3]

◆ GetValueRGB() [3/3]

◆ ImagesToStack()

◆ ImportROIsCSV()

◆ Initialize()

◆ isOME()

◆ isOMESeries()

◆ isTiffSeries()

◆ LevelFromResolution()

◆ MergeChannels() [1/2]

◆ MergeChannels() [2/2]

◆ MergeT()

◆ MergeZ()

◆ Open() [1/2]

◆ Open() [2/2]

◆ OpenAsync() [1/2]

◆ OpenAsync() [2/2]

◆ OpenFile() [1/4]

◆ OpenFile() [2/4]

◆ OpenFile() [3/4]

◆ OpenFile() [4/4]

◆ OpenOME() [1/3]

◆ OpenOME() [2/3]

◆ OpenOME() [3/3]