BioGTK  5.0.1
A .NET library & program for annotating, editing various microscopy imaging formats using Bioformats supported images. Including whole slide, pyramidal, and series.
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BioGTK Documentation

BioGTK

A .NET application & library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Check out the wiki for library usage. or check out the documentation. Supports Windows, Linux and Mac. For Windows & Mac see installation instructions. For Discussion check out the new Discord Server. https://discord.gg/tdeyc6fgpv

NuGet version (BioGTK) NuGet version (BioGTK) DOI

Features

Dependencies

Scripting

Plugins

Models

Mac Installation

Windows Installation

Linux Installation

Examples

First you need to setup your project as a GTK project with .NET 8.0 as the target. Then in between Gtk.Application.Init() and Gtk.Application.Run() use the library as you please. Here is an example for opening a new NodeView from BioGTKApp program.cs.

Console.WriteLine("Initializing GTK.");
Gtk.Application.Init();
Console.WriteLine("Creating NodeView.");
BioGTK.NodeView node = BioGTK.NodeView.Create(args);
node.Show();
Gtk.Application.Run();

Another example on how to open an image with a new ImageView

Gtk.Application.Init();
//Since we will be using the GUI we call App.Initialize();
App.Initialize();
BioImage bm = BioImage.OpenFile("F:\\TESTIMAGES\\CZI\\16Bit-ZStack.czi");
ImageView v = ImageView.Create(bm);
v.Show();
Gtk.Application.Run();

Usage

//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 = NodeView.Create(new string[]{"file"});

//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);

//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();

//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();

//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();

Sample Plugin

using AForge;
using BioGTK;
using Gdk;
using Gtk;
using SkiaSharp.Views.Desktop;
namespace PluginExample
{
    public class PluginExample : BioGTK.Plugin.IPlugin
    {
        public string Name => "PluginExample";
        public string MenuPath => "Tools/" + Name + ".dll";
        public bool ContextMenu => false;
        public void Execute(string[] args)
        {
        }
        public void KeyUpEvent(object o, KeyPressEventArgs e)
        {
        }
        public void KeyDownEvent(object o, KeyPressEventArgs e)
        {
        }
        public void ScrollEvent(object o, ScrollEventArgs args)
        {
        }
        public void Render(object sender, SKPaintSurfaceEventArgs e)
        {
        }
        public void MouseMove(object o, PointD e, MotionNotifyEventArgs buts)
        {
        }
        public void MouseUp(object o, PointD e, ButtonReleaseEventArgs buts)
        {
        }
        public void MouseDown(object o, PointD e, ButtonPressEventArgs buts)
        {
        }

    }
}

Sample Tool Script

//css_reference BioGTK.dll; 
using System; 
using BioGTK;
using System.Threading;
using AForge;
using Gdk;
public class Loader {

//Point ROI Tool Example
public string Load()
{
    int ind = 1;
    do
    {
        BioGTK.Scripting.State s = BioGTK.Scripting.GetState();
        if (s != null)
        {
            if (!s.processed)
            {
                if (s.type == BioGTK.Scripting.Event.Down && s.buts == 1)
                {
                    ZCT cord = BioGTK.App.viewer.GetCoordinate();
                    BioGTK.Scripting.LogLine(cord.ToString() + " Coordinate");
                    BioGTK.ROI an = BioGTK.ROI.CreatePoint(cord, s.p.X, s.p.Y);
                    BioGTK.ImageView.SelectedImage.Annotations.Add(an);
                    BioGTK.Scripting.LogLine(cord.ToString() + " Coordinate");
                    an.Text = "Point" + ind;
                    ind++;
                    BioGTK.Scripting.LogLine(s.ToString() + " Point");
                }
                else
                if (s.type == BioGTK.Scripting.Event.Up)
                {
                    BioGTK.Scripting.LogLine(s.ToString());
                }
                else
                if (s.type == BioGTK.Scripting.Event.Move)
                {
                    BioGTK.Scripting.LogLine(s.ToString());
                }
                if(s.key == Key.r)
                {
                    BioGTK.Scripting.LogLine("KeyDown");
                }
                s.processed = true;
            }
        }
        if(BioGTK.Scripting.Exit("test.cs"))
        {    
            return "OK";
        }
    } while (true);
    return "OK";
}
}