imagej

ImageJ - Trigger event when frame in ImageStack is changed

由 岁酱吖の 提交于 2019-12-08 11:13:13
问题 I'm trying to make an ImageJ plugin that generates a stack of masks based on a selection in each frame in an active stack. To do that, I need to clear the mask and save it when the frame in the stack changed. I don't see any event options available on the API for ImageStack; how would I trigger a sequence of steps when the stack frame is changed? Is there an event to do this? 回答1: The event options are implemented in the ImagePlus class, not in the ImageStack . Your plugin should implement

ImageJ package for R [closed]

由 我们两清 提交于 2019-12-07 22:56:58
问题 Closed. This question is off-topic. It is not currently accepting answers. Want to improve this question? Update the question so it's on-topic for Stack Overflow. Closed 4 years ago . I'm looking for an integration of ImageJ and R. There was a package called RImageJ as referenced in [1][2] for previous versions of R (I'm using R 3.1.2 (2014-10-31) -- "Pumpkin Helmet" ) but it isn't available anymore. Basically what I'd like to try is a region growing algorithm over an image in R. Does anybody

How do I save the XY coordinates of a Binary Image in R?

由 喜欢而已 提交于 2019-12-07 22:41:07
问题 I am trying to save the XY coordinates of a binary image in R similarly to the save "Save XY Coordinates" function in ImageJ. I've looked through several image analysis packages available for R, but haven't yet figured out how to accomplish this. 回答1: There are many ways to do the following in R: img_fil <- "~/data/ZjYqw.jpg" img <- magick::image_read(img_fil) img_df <- RSAGA::grid.to.xyz(as.matrix(as.raster(img))) head(img_df) ## x y z ## 1 0 599 #ffffff ## 2 1 599 #ffffff ## 3 2 599 #ffffff

ImageJ - How to import and display a mesh?

由 放肆的年华 提交于 2019-12-06 13:28:02
问题 How can one open and display a mesh (either using the .obj, .stl or .dxf formats) on ImageJ? I have tried to open the files through file/open but got nothing displaying using the 3DViewer or the Interactive 3D Surface Plot plugins? I did get the list on the image below when I opened the obj... I had a look at the tutorials and this paper. 回答1: I guess you opened it using ImageJ's File->Open command. You should instead open the 3D Viewer first and click on File->Import surfaces->Wavefront (for

How do I save the XY coordinates of a Binary Image in R?

由 蹲街弑〆低调 提交于 2019-12-06 11:14:29
I am trying to save the XY coordinates of a binary image in R similarly to the save "Save XY Coordinates" function in ImageJ. I've looked through several image analysis packages available for R, but haven't yet figured out how to accomplish this. There are many ways to do the following in R: img_fil <- "~/data/ZjYqw.jpg" img <- magick::image_read(img_fil) img_df <- RSAGA::grid.to.xyz(as.matrix(as.raster(img))) head(img_df) ## x y z ## 1 0 599 #ffffff ## 2 1 599 #ffffff ## 3 2 599 #ffffff ## 4 3 599 #ffffff ## 5 4 599 #ffffff ## 6 5 599 #ffffff 来源： https://stackoverflow.com/questions/39562605

ImageJ package for R [closed]

由 ぃ、小莉子 提交于 2019-12-06 10:17:53
Closed. This question is off-topic . It is not currently accepting answers. Want to improve this question? Update the question so it's on-topic for Stack Overflow. Closed 4 years ago . I'm looking for an integration of ImageJ and R. There was a package called RImageJ as referenced in [1][2] for previous versions of R (I'm using R 3.1.2 (2014-10-31) -- "Pumpkin Helmet" ) but it isn't available anymore. Basically what I'd like to try is a region growing algorithm over an image in R. Does anybody know about an updated version of RImageJ or another package allowing this algorithm?. Thanks ;) [1]

Create JavaFX Image from PGM or TIFF as fast as possible

由 情到浓时终转凉″ 提交于 2019-12-06 09:43:44
问题 I'm capturing images from a scanner device with java. The input format ist PGM or TIFF. I have to show up live results in the user interface. Actually I'm using ImageJ to read the source input stream as tiff, because ImageJ can also handle incomplete streams. After that the ImagePlus object is converted into a BufferedImage and finally into a JavaFX Image . ImagePlus imagePlus = new Opener().openTiff(inputStream, ""); BufferedImage bufferedImage = imagePlus.getBufferedImage(); Image image =

How to specify colormap when saving tiff stack

由 南楼画角 提交于 2019-12-06 04:49:28
I'm using tifffile in python to save out 3-channel tiff stacks, which I then want to read into ImageJ or FIJI. These tiff stacks open as composites in ImageJ with each channel assigned a (presumably default) colormap/LUT. However, the colors that are assigned aren't the colors that make sense for my images. My problem is that I can't figure out how to specify the colormap for each channel when saving the image using tifffile . For example, I'd like to have the following colormap assignments: ch 0: grays ch 1: green ch 2: red Here's the code that I'm using to save the files: # save hyperstack

Twain device (scanner) control in Java

由 拥有回忆 提交于 2019-12-04 23:44:27
I want to scan a number of papers through Java. I found the mm's computing twain library . When I run the example TwainExample.java at the site, I receive this error. uk.co.mmscomputing.device.twain.TwainIOException: Cannot load Twain Source Manager. On the other hand, almost the same code works with ImageJ as a plugin . Yet, when I used this code by itself I still receive the same exception. I wonder why this is not working. You can try download TWAINDSM.DLL for 64bit and put it in C:/windows/system32, or 32 if you have it. Find it on SourceForge Regards In the past I've used Morena library

Create JavaFX Image from PGM or TIFF as fast as possible

由 徘徊边缘 提交于 2019-12-04 19:02:39
I'm capturing images from a scanner device with java. The input format ist PGM or TIFF. I have to show up live results in the user interface. Actually I'm using ImageJ to read the source input stream as tiff, because ImageJ can also handle incomplete streams. After that the ImagePlus object is converted into a BufferedImage and finally into a JavaFX Image . ImagePlus imagePlus = new Opener().openTiff(inputStream, ""); BufferedImage bufferedImage = imagePlus.getBufferedImage(); Image image = SwingFXUtils.toFXImage(bufferedImage, null); This is very slow. I need a faster way to create the JavaFX
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