Merge branch 'main' of https://github.com/BiologyTools/BioLib

README.md

@@ -1,4 +1,66 @@
 # BioLib
 ![Nuget](https://img.shields.io/nuget/dt/BioLib) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8127022.svg)](https://doi.org/10.5281/zenodo.8127022)
 
-A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac.
+A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac. Check out the [documentation.](https://biologytools.github.io/Documentation/BioLib-1.8.0/html/index.html)
+
+## Usage
+```
+//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 = 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 = ImageView.Create(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));
+
+//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");
+
+//To convert between different pixel formats we can call for example To24Bit.
+b.To24Bit();
+```