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Bio is an application \u0026 library for editing \u0026 annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters \u0026 macro functions. Check out the wiki for [library usage.](https://github.com/BiologyTools/Bio/wiki/Library-Usage) or check out the [documentation.](https://biologytools.github.io/Documentation/BioCore/index.html)\n\n[![NuGet version (BioCore)](https://img.shields.io/nuget/v/BioCore.svg?style=flat-square)](https://www.nuget.org/packages/BioCore/3.4.0)\n[![NuGet version (BioCore)](https://img.shields.io/nuget/dt/BioCore?color=g)](https://www.nuget.org/packages/BioCore/3.4.0) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8207863.svg)](https://doi.org/10.5281/zenodo.8207863)\n## Features\n\n- C# scripting with sample tool-script and other sample scripts in \"/Scripts/\" folder. [See samples](https://github.com/BioMicroscopy/BioImage-Scripts)\n\n- Supports running ImageJ macro commands on images open in Bio. New Console to run ImageJ macro commands and Bio C# functions.\n\n- Supports Pyramidal images with multiple resolutions. Like whole slide images.\n\n- Stitch images at varying resolutions into single pyramidal image with multiple resolutions.\n\n- Multiple view modes like Emission, and Filtered. ROI's shown for each channel can be configured in ROI Manager.\n\n- Supports drawing shapes \u0026 colors onto 16 bit \u0026 48 bit images, unlike System.Drawing.Graphics.\n\n- Convenient viewing of image stacks with scroll wheel moving Z-plane and mouse side buttons scrolling C-planes.\n\n- Editing \u0026 saving ROI's in images to OME format image stacks.\n\n- Copy \u0026 Paste to quickly annotate images and name them easily by right click.\n\n- Select multiple points by holding down control key, for delete \u0026 move tools. \n\n- Exporting ROI's from each OME image in a folder of images to CSV.\n\n- Easy freeform annotation with magic select tool which selects based on blob detection.\n\n- Use AForge filters by opening filters tool window and right click to apply. Currently supports only some AForge filters as many of them do not support 16bit and 48bit images. Convert to 8bit image to make use of more filters. Applyed filters can be easily recorded and used in scripts. Bio impliments some filters like crop for 16 \u0026 48 bit images.\n\n- `Star this project on Github to help spread the word about Bio!`\n\n## Dependencies\n- [BioFormatsNET8](https://github.com/BiologyTools/BioFormatsNET8)\n- [IKVM](http://www.ikvm.net/)\n- [AForge](http://www.aforgenet.com/)\n- [LibTiff.Net](https://bitmiracle.com/libtiff/)\n- [Cs-script](https://github.com/oleg-shilo/cs-script/blob/master/LICENSE)\n- [ImageJ](https://imagej.nih.gov/ij/) (Only needed when running ImageJ macro commands)\n- [OpenSlideGTK](https://github.com/BiologyTools/OpenSlideSharp) (Optional) [MIT](https://github.com/BiologyTools/OpenSlideSharp/blob/master/LICENSE)\n\n## Licenses\n- Bio [GPL3](https://www.gnu.org/licenses/gpl-3.0.en.html)\n- AForge [LGPL](http://www.aforgenet.com/framework/license.html)\n- BioFormatsNet6 [GPL3](https://www.gnu.org/licenses/gpl-2.0.en.html)\n- [IKVM](https://github.com/gluck/ikvm/blob/master/LICENSE)\n- LibTiff.Net [BSD](https://bitmiracle.com/libtiff/)\n- Cs-script [MIT](https://github.com/oleg-shilo/cs-script/blob/master/LICENSE)\n\n## Installation\n- Optionally install [OpenSlide](https://openslide.org/docs/windows/) for increased performance.\n\n## Scripting\n-  Save scripts into \"StartupPath/Scripts\" with \".cs\" ending.\n-  Open script editor and recorder from menu.\n-  Double click on script name in Script runner to run script.\n-  Scripts saved in Scripts folder will be loaded into script runner.\n-  Program installer include sample filter \u0026 tool script.\n-  Use Script recorder to record program function calls and script runner to turn recorder text into working scripts. (See sample [scripts](https://github.com/BioMicroscopy/BioImage-Scripts)\n\n## Plugins\n- Save plugin DLL's into \"StartupPath/Plugins\"\n- See [example plugin](https://github.com/BiologyTools/PluginExampleWIN) to create your own plugins.\n\n## Sample Tool Script\n```\n//css_reference BioCore.dll;\nusing System;\nusing System.Windows.Forms;\nusing System.Drawing;\nusing Bio;\nusing System.Threading;\n\npublic class Loader\n{\n\n\t//Point ROI Tool Example\n\tpublic string Load()\n\t{\n\t\tint ind = 1;\n\t\tdo\n\t\t{\n\t\t\tBio.Scripting.State s = Bio.Scripting.GetState();\n\t\t\tif (s != null)\n\t\t\t{\n\t\t\t\tif (!s.processed)\n\t\t\t\t{\n\t\t\t\t\tif (s.type == Bio.Scripting.Event.Down \u0026\u0026 s.buts == MouseButtons.Left)\n\t\t\t\t\t{\n\t\t\t\t\t\tZCT cord = Bio.App.viewer.GetCoordinate();\n\t\t\t\t\t\tBio.Scripting.LogLine(cord.ToString() + \" Coordinate\");\n\t\t\t\t\t\tBio.ROI an = Bio.ROI.CreatePoint(cord, s.p.X, s.p.Y);\n\t\t\t\t\t\tBio.ImageView.SelectedImage.Annotations.Add(an);\n\t\t\t\t\t\tBio.Scripting.LogLine(cord.ToString() + \" Coordinate\");\n\t\t\t\t\t\tan.Text = \"Point\" + ind;\n\t\t\t\t\t\tind++;\n\t\t\t\t\t\tBio.Scripting.LogLine(s.ToString() + \" Point\");\n\t\t\t\t\t\t//ImageView.viewer.UpdateOverlay();\n\t\t\t\t\t}\n\t\t\t\t\telse\n\t\t\t\t\tif (s.type == Bio.Scripting.Event.Up)\n\t\t\t\t\t{\n\t\t\t\t\t\tBio.Scripting.LogLine(s.ToString());\n\t\t\t\t\t}\n\t\t\t\t\telse\n\t\t\t\t\tif (s.type == Bio.Scripting.Event.Move)\n\t\t\t\t\t{\n\t\t\t\t\t\tBio.Scripting.LogLine(s.ToString());\n\t\t\t\t\t}\n\t\t\t\t\ts.processed = true;\n\t\t\t\t}\n\t\t\t}\n\t\t} while (true);\n\t\treturn \"OK\";\n\t}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiologytools%2Fbiocore","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiologytools%2Fbiocore","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiologytools%2Fbiocore/lists"}