Library Usage

//For BioGTK and BioCore if you want to initialize the application call app initialize. This will initialize Bioformats library as well as the rest of the application.
App.Initialize();

//Or you can create a new NodeView which will initialize the application as well as parse any command line arguments.
NodeView nodes = new NodeView(new string[]{"file"});

//For BioGTK, BioCore, and BioLib you can also call BioImage.Initialize to initialize just the Bioformats library.
BioImage.Initialize();

//Once initialized you can open OME, ImageJ tiff files, and Bio Tiff files with:
BioImage b = BioImage.OpenFile("file");

//Or if you want to use specifically the OME image reader you can use BioImage.OpenOME
BioImage b = BioImage.OpenOME("file");

//If you are working with a pyramidal image you can open a portion of a tiled image with OpenOME.
//BioImage.OpenOME(string file, int serie, bool tab, bool addToImages, bool tile, int tilex, int tiley, int tileSizeX, int tileSizeY)

//You can specify whether to open in a newtab as well as whether to add the image to the Images.images table. As well as specify whether to open as a tile with the specified tile X,Y position & tile width & height.    
BioImage.OpenOME("file",0,false,false,true,0,0,600,600);
//This will open a portion of the image as a tile and won't add it to the Images table.

//Once you have opened a tiled image with BioImage.OpenOME you can call the GetTile(BioImage b, ZCT coord, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY) method to quickly get another tile from different portion of the image. For BioGTK & BioLib
Bitmap bm = GetTile(b, new ZCT(0,0,0), 0, 100, 100, 600, 600);
//For BioCore
BufferInfo bi = GetTile(b, new ZCT(0,0,0), 0, 100, 100, 600, 600);

//You can display an image with the ImageView control which can display Pyramidal, Whole-Slide, and Series of images.
ImageView v = new ImageView(b);

//To get the current coordinate of the ImageView you can call GetCoordinate.
ZCT cord = v.GetCoordinate();
//or to set the current coordinate
v.SetCoordinate(new ZCT(1,1,1));

//To create a point as well as any other ROI type you can call the ROI create methods.
ROI p = ROI.CreatePoint(cord, 0, 0);
ROI rect = ROI.CreateRectangle(cord, 0, 0, 100, 100);

//Usage of Graphics class for 16 & 48 bit images as well as regular bit depth images is very similar to System.Graphics.
//We create a new Graphics object by passing the Bitmap for BioGTK & BioLib and BufferInfo for BioCore
Graphics g = Graphics.FromImage(b.Buffers[0]);

//Then we create a pen by passing a ColorS which represent a Color with, a higher bit depth (unsigned short) rather than a byte.
g.pen = new Pen(new ColorS(ushort.MaxValue, ushort.MaxValue, ushort.MaxValue),10,b.bitsPerPixel);

//Then we can call the familiar methods DrawLine, DrawPolygon, FillPolygon etc.
g.DrawLine(0,0,100,100);
//Finally we dispose the Graphics object.
g.Dispose();

//Then to update the image in the viewer once we have made changes to the image we call:
v.UpdateImage();
//This will update the images of the viewer in the current coordinate plane.
v.UpdateView();
//Then we can call UpdateView to refresh the view.
v.UpdateView();

//We can also save the resulting image given the ID of the image in the Images table.
//All images opened with BioImage.OpenFile or BioImage.OpenOME are added to the Images.images table with the filename as an ID.
BioImage.SaveFile("file","path");

//To convert between different pixel formats we can call for example ToRGB24
b.ToRGB24();