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

Features

• C# scripting with sample tool-script and other sample scripts in "/Scripts/" folder. See samples.

• Supports running ImageJ macro commands on images open in Bio. Console to run ImageJ macro commands and Bio C# scripts.

• Supports viewing & creating pyramidal images with multiple resolutions. Like whole slide images.

• Stitch images at varying resolutions into single pyramidal image with multiple resolutions.

• Multiple view modes like Emission, and Filtered. ROI's shown for each channel can be configured in ROI Manager.

• Supports drawing shapes & colors onto 16 bit & 48 bit images, unlike System.Drawing.Graphics.

• Convenient viewing of image stacks with scroll wheel moving Z-plane and mouse side buttons scrolling C-planes.

• Editing & saving ROI's in images to OME format image stacks.

• Copy & Paste to quickly annotate images and name them easily by right click.

• Select multiple points by holding down control key, and move them by holding down control key.

• Exporting ROI's from each OME image in a folder of images to CSV.

• Easy segmentation with Segment Anything 2 (SAM-2) or Micro-SAM. Download required model files from here for SAM-2. and here for Micro-SAM placing them in the "StartUpPath" folder of the program.

Dependencies

• BioFormats.NET8 GPL3
• IKVM License
• AForge LGPL
• LibTiff.Net BSD
• Cs-script MIT
• ImageJ (Only needed when running ImageJ macro commands)
• ScottPlot MIT
• LibVips (Optional) LGPL
• Segment-Anything-CSharp (Optional) Apache License 2.0
• ONNX-SAM2-Segment-Anything (Optional) MIT
• OpenSlideGTK (Optional) MIT

Scripting

• Save scripts into "StartupPath/Scripts" with ".cs" ending.
• Open script editor and recorder from menu.
• Scripts saved in Scripts folder will be loaded into script runner.
• Use Script recorder to record program function calls and script runner to turn recorder text into working scripts. (See sample scripts

Plugins

• Save plugin DLL's into "StartupPath/Plugins"
• Add plugins from Github repositories by clicking Update and add the url of the repository which you want to add.
• See example plugin to create your own plugins.
• Add the BioGTK plugin repository "https://github.com/BiologyTools/BioGTK-Plugins" to your updater list.

Models

• Save models into "StartupPath/Models" supports BioImage.IO models.
• Supports ONNX (".onnx") and PyTorch models (".pt"). For PyTorch models include the ".yaml" metadata file with the same name as the model file in the models folder.

Mac installation,

• See this video or follow the instructions below.
• Install Mac package manager homebrew.
• From brew install GTK3.
• Download the BioGTK application for either OSX-x64 or OSX-Arm from releases.
• Make the .app bundle executable by opening terminal in the Contents/MacOS folder then run "chmod 755 BioGTKApp" then drag it into the applications folder.
• Optionally install OpenSlide for better navigation of whole-slide-images.
• Optionally install LibVips for increased performance and functions with whole-slide-images.
• Optionally for SAM install ONNX Runtime by running "brew install onnxruntime".

Windows Installation

• See this video or follow the instructions below.
• Install package manager MSYS2. to install package GTK3. (Required for GTK Apps.)
• Download the BioGTK Windows installer from releases.
• Optionally install OpenSlide for better navigation of whole-slide-images. Be sure to set the PATH variable correctly.
• Optionally install CUDA for hardware accelerated stitching as well as tile cache in graphics card memory instead of RAM.
• Optionally install PyTorch for running BioImage.io models.

Linux Installation

• See this video or follow the instructions below.
• Download the latest tarball(tar.gz) from Releases as linux already includes GTK3 package.
• Extract the tarball and go to the "Glade" folder and select all the glade files and change permissions to read-write.
• Optionally install LibVips for increased performance and functions with whole-slide-images.
• Optionally install OpenSlide for better navigation of whole-slide-images.
• Optionally install CUDA for hardware accelerated stitching as well as tile cache in graphics card memory instead of RAM.
• Optionally install PyTorch for running BioImage.io models.

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";
}
}