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). Download required model files from here. Renaming them to "decoder-quant.onnx" and "encoder-quant.onnx" then 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

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"
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

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

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";
}
}

BiologyTools / BioGTK