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Search everywhere only in this topic. Advanced Search. Classic List Threaded. Gabriel Landini. Saving a stack to. STL format? Hi, Does anybody know of an application or plugin or library that can convert a binary stack a volume into a STL file? STL files are used for rapid prototyping 3D printers. Thanks Gabriel.

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Michael Doube. Re: Saving a stack to. Gabriel, I don't know of anything both free and good but there are commercial packages of varying quality. The triangle's normal can easily be calculated from the cross-product of two edges. Then it is just a case of writing out the file in the appropriate format.

Looking at the 3D Viewer code, the best place for such a method is probably the MeshExporter class.

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I know Bene is pretty busy right now and so am I, but this would be a very useful function for users of the viewer I have wanted it myself in the past.

Albert Cardona In reply to this post by Gabriel Landini. Blender does : For best experience, save as wavefront in the 3D viewer, and load into Blender via "File - import - wavefront obj ". Be careful not to limit the size of your object to "10", or to merge the multiple objects. Read the import dialog with attention.Dear Forum, I am as new as they come when it comes to ImageJ, and would greatly appreciate assistance on this. Let me look into doing that…. Until I add this to the main version of 3D viewer, you can get my version of 3D viewer which works exactly the same as the current 3D viewer with couple of extra features from the Funimage update site.

You will get a dialog asking you to set the dimensions of the output image.

imagej stl

This is what the output looks like:. The output is an image with voxels filled in along the surface. Hey, thanks for getting back to me. Did you move the version of 3D viewer that was already there? If you use update sites in FIJI this would be taken care of automatically, but you will need to move the older version manually out of the plugins directory otherwise.

The version on the update site is setup to be handled by the FIJI updater, which would have done this renaming for you.

Very nice plugin, thanks for the help!

imagej stl

Good, I was just about to reply asking you to please not try to install stuff manually. We did a whole lot of work in ImageJ2 to make installation simple, so why not use it? Is the color set? Changing the color can be kind of confusing: double-click the dropper icon in the ImageJ bar and change it to something like a mid-level gray.

It also automatically determines which regions to fill. I may have been mistaken about the library providing the flood fill. This would be the one you want. Yes, I have some similar use cases. This would fit in with the general thrust to decouple processing from display - at the moment, the 3D Viewer requires an intermediate display step which is not necessary and sometimes breaks the processing pipeline usually because the data is too big for the GPU.

Yeah, dissecting 3D viewer is also on the agenda. STL file into stack of images Image Analysis. Regards, Ahmed. Fractal Dimension of STL mesh. Which input file format for 3D data?

Unable to convert stl to stacks. Error with converting mesh to image. Should be on the Funimage update site now. Glad it is working.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again.

Colocalisation tutorial using ImageJ

If nothing happens, download the GitHub extension for Visual Studio and try again. The plugin is a filter that takes an image, copies it and converts it to grayscale, then uses the data to produce an STL format file suitable for 3D printing. It creates a surface using these, treating brighter value pixels as higher points. Before doing that, it creates a "floor" and "walls" both required to facilitate 3D printability. The program attempts to preserve as much information as is reasonable.

To the best of my knowledge, it loses no information from the grayscale image copy to the STL.

3D Viewer and exporting STL files

There is some loss going from the original image to grayscale, because the plugin uses only 8-bit grayscale. Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Sign up. Java Branch: master. Find file. Sign in Sign up. Go back. Launching Xcode If nothing happens, download Xcode and try again. Latest commit Fetching latest commit…. Details on How the Program Works: Information Preservation The program attempts to preserve as much information as is reasonable.

Installing the Plug-in download the files Locate the ImageJ "plugins" folder, which is in the top-level folder of your ImageJ installation. The name has to match the title of the ". Copy or move the ". Open ImageJ, open an image that you would like to use the plugin on. Select the file and click "Open" -- the program should compile.

ImageJ Features

You signed in with another tab or window.Open Source: ImageJ and its Java source code are freely available and in the public domain. No license is required. User Community: ImageJ has a large and knowledgeable worldwide user community.

More than users and developers subscribe to the ImageJ mailing list. Macros: Automate tasks and create custom tools using macros.

imagej stl

Generate macro code using the command recorder and debug it using the macro debugger. More than macros are available on the ImageJ Web site. More than plugins are available. Toolkit: Use ImageJ as a image processing toolkit class library to develop applets, servlets or applications. Speed: ImageJ is the world's fastest pure Java image processing program. It can filter a x image in 0. That's 40 million pixels per second! Data Types: 8-bit grayscale or indexed color, bit unsigned integer, bit floating-point and RGB color.

Open and save many other formats using plugins. Image display: Tools are provided for zooming to and scrolling images. All analysis and processing functions work at any magnification factor. Selections: Create rectangular, elliptical or irregular area selections. Create line and point selections. Edit selections and automatically create them using the wand tool.

Draw, fill, clear, filter or measure selections. Save selections and transfer them to other images. Image Enhancement: Supports smoothing, sharpening, edge detection, median filtering and thresholding on both 8-bit grayscale and RGB color images.

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Interactively adjust brightness and contrast of 8, 16 and bit images. Geometric Operations: Crop, scale, resize and rotate. Flip vertically or horizontally. Analysis: Measure area, mean, standard deviation, min and max of selection or entire image.

Measure lengths and angles. Use real world measurement units such as millimeters. Calibrate using density standards. Generate histograms and profile plots.

医用画像位置合わせの基礎⑤~Fiji pluginを用いた画像位置合わせ~

Editing: Cut, copy or paste images or selections. Add text, arrows, rectangles, ellipses or polygons to images. Merge 8-bit components into a color image. Convert an RGB image to 8-bit indexed color. Apply pseudo-color palettes to grayscale images.

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Stacks: Display a "stack" of related images in a single window. Process an entire stack using a single command. Open a folder of images as a stack. Save stacks as multi-image TIFF files.Feedback is appreciated thank you! This process can be used for drawings, logos, or whatever image you might want to try it on.

To test it out I converted the EngineerDog Logo into a coaster in a single sitting. This article will walk you through the process I used step by step. The main Enginerdog Logo was created for me by talented animation artist Jesse J Jonesso selected because I love his work. I copied the image and pasted into a Microsoft Paint window so I could make the unsophisticated edits that I am able to.

I found a public domain image of a wench from google and modified it to my liking. Again I colored it in using MS Paint. The next step is to edit the image to increase the contrast so I can see where all the edges are. Those are the only two possibilities. In my logo image the dog collar was a mid-range color and ended up creating a line of contrast too thin to 3D print, so I used a paint brush tool to better define the collars perimeter.

You can use the Convertio.

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Good to have multiple options in case something goes wrong or a link dies over time. If you have a laser cutter then at this point you are done because this file type can easily be used in laser cutting software to generate g-code and zap your picture on everything. If you want to 3D print it then read on. The next step is also an easy one.

STL file types are normally difficult to work with; they are kind of like the pdf of the 3d world. In this demo all I did to the logo was resize it as needed. So I had to either print it big or else go back to step one and cover all the outlines with a thicker paintbrush. I chose a mm diameter disc to create a coaster.

After that I selected the resulting disc and my logo, then grouped again.Fiji is an image processing package — a "batteries-included" distribution of ImageJbundling many plugins which facilitate scientific image analysis. More Downloads Cite Contribute. Fiji is easy to use and install - in one-click, Fiji installs all of its plugins, features an automatic updater, and offers comprehensive documentation.

Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating. Like ImageJ itself, Fiji is an open source project hosted on GitHubdeveloped and written by the community.

Fiji features thousands of plugins that aid in scientific image processing and analysis. Here are a few featured plugins hand-picked by the Fiji community - refresh the page to see different plugins! List of All Plugins. Fiji is developed by contributors around the worldand funded from various sources.

Fiji is an open source project, so everybody is welcome to contribute with plugins, patches, bug reports, tutorials, documentation, and artwork. Read more. The Fiji project is driven by a strong desire to improve the tools available for life sciences to process and analyze data. To this end, Fiji collaborates closely with the following projects:. Plugins and other components have their own licenses.

Like most scientific software, funding for the Fiji project is driven by citations. If you use Fiji, please cite it in your publications! Fiji Home current Wiki Source Forum. Fiji Fiji is an image processing package — a "batteries-included" distribution of ImageJbundling many plugins which facilitate scientific image analysis.

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Plugins Fiji features thousands of plugins that aid in scientific image processing and analysis. Contributors Fiji is developed by contributors around the worldand funded from various sources. Read more Partnered Projects The Fiji project is driven by a strong desire to improve the tools available for life sciences to process and analyze data.

To this end, Fiji collaborates closely with the following projects: ImageJ2. Tweets by FijiSc.Fiji is a distribution of ImageJ which includes many useful plugins contributed by the community.

We used to offer Debian packages of Fiji. Unfortunately, for a variety of reasons, we are withdrawing support for these packages until such time as someone is able to maintain them properly, so please switch to using the Linux downloads above instead. If you are a Debian packaging expert who would like to address this situation, we would love to have your help—please join us in chat or on the forum. Fiji is distributed as a portable application. That means that you do not have to run an installer; just download, unpack and start it.

See the source code page for details on obtaining the Fiji source code. You can download previous Fiji builds by date stamp from the archive. This sections offers older downloads of Fiji, preserved just prior to introducing major changes.

The idea is that if something goes horribly wrong, you can fall back to a stable version. Skip to contentSkip to search. ImageJ From ImageJ. Page Discussion View source History. Caution: " Program Files " not recommended! This page was last modified on 5 Decemberat Create account Log in. No JRE. If you move ImageJ. Just prior to starting the transition to Java 8.

Just prior to a big update to facilitate reproducible builds. Just prior to some big changes to ImageJ2 under the hood.


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