BioGTK 3.8.1

There is a newer version of this package available.
See the version list below for details.
dotnet add package BioGTK --version 3.8.1
NuGet\Install-Package BioGTK -Version 3.8.1
This command is intended to be used within the Package Manager Console in Visual Studio, as it uses the NuGet module's version of Install-Package.
<PackageReference Include="BioGTK" Version="3.8.1" />
For projects that support PackageReference, copy this XML node into the project file to reference the package.
paket add BioGTK --version 3.8.1
#r "nuget: BioGTK, 3.8.1"
#r directive can be used in F# Interactive and Polyglot Notebooks. Copy this into the interactive tool or source code of the script to reference the package.
// Install BioGTK as a Cake Addin
#addin nuget:?package=BioGTK&version=3.8.1

// Install BioGTK as a Cake Tool
#tool nuget:?package=BioGTK&version=3.8.1


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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.

NuGet version (BioGTK) NuGet version (BioGTK) DOI


  • 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 (SAM). Required model files downloadable from Releases.




  • 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

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 file executable by opening terminal in the extracted folder and running "chmod 755 BioGTKApp"
  • Optionally install LibVips package for whole-slide support with homebrew.
  • Optionally install Onnx Runtime by running "brew install onnxruntime" for running SAM.

Windows Installation

  • Install package manager MSYS2. to install package GTK3. (Required for GTK Apps.)
  • Download the BioGTK Windows installer from releases.
  • Optionally install LibVips for increased performance when opening pyramidal images. Make sure to define environmental variable $VIPS_HOME as instructed here.

Linux Installation

  • Just download the latest tarball(tar.gz) from Releases as linux already includes GTK3 package.
  • Optionally install LibVips for increased performance when opening pyramidal images.


//First you need to setup your project as a GTK project with .NET 6.0 as the target. 
//Then in between Gtk.Application.Init() and Gtk.Application.Run() use the library as you please.
//Here is an example from BioGTKApp program.cs.

Console.WriteLine("Initializing GTK.");
Console.WriteLine("Creating NodeView.");
BioGTK.NodeView node = BioGTK.NodeView.Create(args);

//If you want to initialize the application call app initialize. 
//This will initialize Bioformats library as well as the rest of the application.

//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.

//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.    
//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.
//Finally we dispose the Graphics object.

//Then to update the image in the viewer once we have made changes to the image we call:
//This will update the images of the viewer in the current coordinate plane.

//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.

//To convert between different pixel formats we can call for example To24Bit.

Sample Tool Script

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

//Point ROI Tool Example
public string Load()
	int ind = 1;
		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.Scripting.LogLine(cord.ToString() + " Coordinate");
					an.Text = "Point" + ind;
					BioGTK.Scripting.LogLine(s.ToString() + " Point");
				if (s.type == BioGTK.Scripting.Event.Up)
				if (s.type == BioGTK.Scripting.Event.Move)
				s.processed = true;
			return "OK";
	} while (true);
	return "OK";
Product Compatible and additional computed target framework versions.
.NET net6.0 is compatible.  net6.0-android was computed.  net6.0-ios was computed.  net6.0-maccatalyst was computed.  net6.0-macos was computed.  net6.0-tvos was computed.  net6.0-windows was computed.  net7.0 was computed.  net7.0-android was computed.  net7.0-ios was computed.  net7.0-maccatalyst was computed.  net7.0-macos was computed.  net7.0-tvos was computed.  net7.0-windows was computed.  net8.0 was computed.  net8.0-android was computed.  net8.0-browser was computed.  net8.0-ios was computed.  net8.0-maccatalyst was computed.  net8.0-macos was computed.  net8.0-tvos was computed.  net8.0-windows was computed. 
Compatible target framework(s)
Additional computed target framework(s)
Learn more about Target Frameworks and .NET Standard.

NuGet packages

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Version Downloads Last updated
4.6.0 62 2/19/2024
4.5.2 76 2/17/2024
4.5.1 79 2/15/2024
4.5.0 84 2/13/2024
4.4.0 74 2/10/2024
4.3.0 67 2/2/2024
4.2.0 104 1/14/2024
4.1.0 127 1/4/2024
4.0.0 110 12/26/2023
3.9.1 102 12/2/2023
3.9.0 87 12/1/2023
3.8.1 111 11/8/2023
3.8.0 83 11/2/2023
3.7.1 199 10/26/2023
3.7.0 223 10/22/2023
3.6.2 213 8/30/2023
3.6.1 217 8/22/2023
3.6.0 269 8/19/2023
3.5.3 189 8/17/2023
3.5.1 237 8/12/2023
3.5.0 365 8/10/2023
3.4.0 255 8/6/2023
3.3.3 319 8/4/2023
3.3.2 272 8/1/2023
3.3.1 301 7/6/2023
3.3.0 262 7/4/2023
3.2.0 293 6/29/2023
3.1.1 223 6/28/2023
3.0.0 220 6/20/2023
2.9.0 239 6/13/2023
2.8.0 189 5/15/2023
2.7.2 227 5/5/2023
2.7.1 247 4/29/2023
2.7.0 232 4/29/2023
2.6.2 400 4/3/2023
2.6.1 363 4/1/2023
2.6.0 365 3/12/2023
2.5.0 397 3/7/2023
2.4.1 334 3/4/2023
2.4.0 449 2/28/2023
2.3.0 421 2/27/2023
2.2.0 219 2/23/2023
2.1.1 197 2/17/2023
2.1.0 213 2/15/2023
1.2.0 252 1/31/2023
1.1.0 236 1/29/2023
1.0.0 241 1/29/2023

Added missing glade files & images to nuget package.