//First call BioImage.Initialize to //initialize 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 = BioImage.GetTile(b, new ZCT(0,0,0), 0, 100, 100, 600, 600); //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)); //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(); //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"); //Usage of OMERO class. OMERO.Connect("demo.openmicroscopy.org", 4064, "username", "password"); string[] files = OMERO.GetAllFiles().ToArray(); string[] dbs = OMERO.GetDatasets().ToArray(); string[] fs = OMERO.GetFolders().ToArray(); string[] dbf = OMERO.GetDatasetFiles("CZI").ToArray(); //Usage of QuPath class. QuPath.Project qu = QuPath.OpenProject("test.qpproj"); BioImage[] bms = new BioImage[] { BioImage.OpenFile("test.ome.tif") }; List<BioImage[]> bims = new List<BioImage[]>(); bims.Add(bms); QuPath.Project qp = QuPath.Project.FromImages(bims, "test.qpproj"); QuPath.Project.SaveProject("myproj.qpproj", bims); //To convert between different pixel formats we can call for example To24Bit. b.To24Bit();