BioGTK 3.5.0

.NET 6.0 This package targets .NET 6.0. The package is compatible with this framework or higher.
There is a newer version of this package available.
See the version list below for details. 
dotnet add package BioGTK --version 3.5.0                

                    
                

            
NuGet\Install-Package BioGTK -Version 3.5.0
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="3.5.0" />
For projects that support PackageReference, copy this XML node into the project file to reference the package. 
paket add BioGTK --version 3.5.0                

                    
                

            
#r "nuget: BioGTK, 3.5.0"
#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=3.5.0

// Install BioGTK as a Cake Tool
#tool nuget:?package=BioGTK&version=3.5.0

BioGTK

alt text

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 new 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

  • 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 Pyramidal images with multiple resolutions. Like whole slide images.

  • 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.

Dependencies

Licenses

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

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.

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.

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;
	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");
					//ImageView.viewer.UpdateOverlay();
				}
				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());
				}
				s.processed = true;
			}
		}
		if(BioGTK.Scripting.Exit("points.cs"))
		{	
			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)
Included target framework(s) (in package)
Learn more about Target Frameworks and .NET Standard.

NuGet packages

This package is not used by any NuGet packages.

GitHub repositories

This package is not used by any popular GitHub repositories.

Version Downloads Last updated
5.6.0 47 10/29/2024
5.5.0 76 10/19/2024
5.4.2 48 10/10/2024
5.4.1 56 10/1/2024
5.4.0 52 9/29/2024
5.3.0 79 8/21/2024
5.2.0 62 7/26/2024
5.1.1 68 5/7/2024
5.1.0 60 4/29/2024
5.0.1 71 4/21/2024
5.0.0 61 4/17/2024
4.9.0 82 3/8/2024
4.8.1 68 3/6/2024
4.8.0 130 3/6/2024
4.7.1 126 2/27/2024
4.7.0 107 2/25/2024
4.6.0 131 2/19/2024
4.5.2 131 2/17/2024
4.5.1 113 2/15/2024
4.5.0 128 2/13/2024
4.4.0 124 2/10/2024
4.3.0 129 2/2/2024
4.2.0 175 1/14/2024
4.1.0 207 1/4/2024
4.0.0 152 12/26/2023
3.9.1 157 12/2/2023
3.9.0 127 12/1/2023
3.8.1 164 11/8/2023
3.8.0 124 11/2/2023
3.7.1 310 10/26/2023
3.7.0 311 10/22/2023
3.6.2 350 8/30/2023
3.6.1 316 8/22/2023
3.6.0 389 8/19/2023
3.5.3 322 8/17/2023
3.5.1 353 8/12/2023
3.5.0 476 8/10/2023
3.4.0 369 8/6/2023
3.3.3 436 8/4/2023
3.3.2 390 8/1/2023
3.3.1 416 7/6/2023
3.3.0 361 7/4/2023
3.2.0 399 6/29/2023
3.1.1 339 6/28/2023
3.0.0 309 6/20/2023
2.9.0 340 6/13/2023
2.8.0 303 5/15/2023
2.7.2 335 5/5/2023
2.7.1 364 4/29/2023
2.7.0 350 4/29/2023
2.6.2 512 4/3/2023
2.6.1 461 4/1/2023
2.6.0 465 3/12/2023
2.5.0 480 3/7/2023
2.4.1 452 3/4/2023
2.4.0 531 2/28/2023
2.3.0 497 2/27/2023
2.2.0 260 2/23/2023
2.1.1 267 2/17/2023
2.1.0 254 2/15/2023
1.2.0 301 1/31/2023
1.1.0 278 1/29/2023
1.0.0 286 1/29/2023

Segment Anything (SAM)