Imagej exception error
Imagej exception error. I am currently trying to upload . Re-start ImageJ. LegacyService at org. I have OlympusViewer plugins, but when I upload the . However, when I run the macro, I am getting the following error: I have seen online on the ImageJ forum that this macro works for other people. Since yesterday, when I added the CLIJ plugin, Fiji crashes when I try to run certain other plugins, such as NanoJ. Any idea what I should do to prevent this? Thank you very much for any help you could provide me! java. g. scijava Delete the ImageJ. When i restart FIJI and try to launch Labkit from existing image open in FIJI, it give that exact same message listed above. Apr 14, 2020 · error handling in ImageJ macro basically means checking if results are present or if image have the right format before an error can happen. in import ImagePlusReader options = ImporterOptions() options. imagej directory (username/Preferences on MacOS). But thanks to the ImageJ Legacy Bridge, most aspects of the original ImageJ work in headless mode, including via PyImageJ when initializing with imagej. ImageMath. DisplayUpdatedEvent Load an image. ImageJ. I have trained in Labkit, run it over a couple of images and am happy with the results. It is the only file changed when you upgrade using the Help>Update ImageJ command. doFit(CurveFitter. 0), and here are two reports Fiji sends me every time I try to update. java:456) Nov 28, 2021 · Hello, I am trying to develop a plugin for fiji/imagej. Isq: For example, if the image that has been opened (by the macro) is not in the required format (TIFF, 3D stack) Oct 24, 2020 · I’m getting the following macro error message when I have done the following: Save a bmp image to a folder; run the macro–choose the folder where my image is saved; Java batch convert saves image to TIFF; choose destination folder. ImageJ Java class. 54i; Java 1. vsi file, it says “Failed to open file Reward B6 VS13 PS13_02. Hope these can help you narrow my problems. io package for many reasons to prevent errors. 0-beta3 to imagej-2. You can also customize the contextual menu that appears when you right click on an image. RuntimeException: java. Could it be that you uploaded at some point without first checking that your Fiji installation is up to date (i. Dec 18, 2020 · Hi, I've been struggling with Fiji integration with the latest version of SimpleITK. measure. For example, using a scanner to read data and receiving an invalid type or writing data into a file that doesn't exist. Jul 9, 2012 · [ERROR] Uncaught exception in thread Thread[plugin thread,6,plugin thread group] java. app/ImageJ-linux32, ImageJ/imagej, ImageJ, and imagej. io(). zip. sc Forum Loading Dec 14, 2017 · I am using the brown fat ROI analyzer on ImageJ and whenever I try to save a group of ROIs i get the error message “java. 1. vsi:jp. The PixelProbe has maintained a reference to some Dataset or View data that is no longer appropriately sized. Copy the above version 1. 53j. To generate run() calls, start the recorder (Plugins/Macro/Record) and run commands from the ImageJ menu bar. This version ij147-jdk6-64bit-setup. For your installation of Fiji, the environment variable should be set to C:\Users\myUserName\Fiji. [ERROR] Exception net. If one of the individual alignment between two images was wrong, this pair will be displaced a lot in the global optimization as all other connecting tiles pull it towards the correct global position. DisplayUpdatedEvent Nov 23, 2023 · It can't run with error for all demos: Exception in thread "main" java. exe Jul 17, 2012 · This is a static HTML version of a legacy ImageJ Trac ticket. I followed the instructions to install the library "imagej" so that I can access Fiji via Anaconda-Python. So your Show would be the following: sitk. IllegalArgumentException: Invalid service: net. I had a zip archive which java. getExtents NOTICE! This is a static HTML version of a legacy ImageJ Trac ticket. Thanks to Kimberly Meechan and Jan Eglinger, ImageJ restores the original look and feel after temporarily using the system look and feel with Windows Jan 1, 1970 · 7 6. Many scale with no problem, however some do not. “Java 1. If running from eclipse you can see the log window receives notice of an exception. formats. allocate(DataTools. ApplicationListener after installing an app event handler Mar 15, 2013 · If you have two or more images open in IJ2 and you exit the program you get an exception and ImageJ does not terminate. 2. The Bio-Formats update site contains nightly builds which may be used for testing new features or getting the latest bug fixes ahead of time. concurrent. If you try to load an original ImageJ class (with package prefix ij), and get a JavaException: Class not found error, this is because the environment was initialized without the original ImageJ included. Contents of ImageJ Folder ij. 14. app\ImageJ-win64. cfg file Restart ImageJ and the launcher (ImageJ. Provide details and share your research! But avoid …. Then open Image Calculator. 2 into the plugins folder. Jan 24, 2020 · To control the version of Java that ImageJ uses, see How do I launch ImageJ with a different version of Java. java:922) at loci. I also tried the daily build (1. I’m using IntelliJ with a maven project (Java 11). Jun 22, 2015 · Runs an ImageJ command, with options that are passed to the GenericDialog and OpenDialog classes. 10. 47. Jan 7, 2023 · Now after a couple of days I am trying to use the Color Profiler plugin, which works perfectly fine when doing individual images, but when I use the same batch macro feature it gives me an Exception error for each image (I will attach the whole error). Jan 11, 2019 · Hi richvaz, Apologies for only spotting your message now. How to troubleshoot problems. 0-SNAPSHOT. NoSuchMethodError or NoClassDefFoundError. SwingDisplayPanel. Please file all new issues there. util Jan 17, 2013 · Both arrays—aPixels_org and aPixels_dup—must have length at least iWidth*iHeight (which is 217156, according to your console output). But it's like the PlanarImg internal reference never updated after the new ImgPlus assigned by add axis plugin. app directory somewhere in your user space (e. Do you have a network connection? Are your proxy settings correct? [ERROR] java. 0-45-generic; 152MB of 15795MB (<1%) java. sc Forum Loading Hi, I am trying to run imagej with a script in spyder however I am getting this issue below. Jan 28, 2020 · Hi, My name is Sammi. init() … Jan 30, 2012 · Exception thrown (below). java:851) at sun. Dec 11, 2018 · Now I am trying to use it to stitch tiles obtained on a Nikon C2 Confocal, and cannot find a combination of baked-in parameters that will allow me to generate a tile, instead I get the following directory error: ERROR: Error: No correlated tiles found, setting the first tile to (0, 0, 0). But if you increase it too much you can’t run two programs at once. java:201 Dec 14, 2017 · Error: java. imagej. jar ij. 45 / ImageJA. May 2, 2017 · Fiji update error - Usage & Issues - Image. I’ve got a few things for you to try. 4) was more straight forward. Oct 11, 2012 · Thanks for the answer. www. lang. createNewStack(Scaler Oct 26, 2011 · The ImageJ project now uses GitHub Issues for issue tracking. ImageJ@72b9dc79 consumed = false Apr 22, 2021 · Just to recap I have tried to use gdb in the develguide. May 10, 2023 · Gerardo Marx Chavez-Campos I'm using the newest version of Fiji (2. jar; Copy the produced jar (e. ImageJ@19d1b44b Jul 16, 2020 · The quickest option would probably be to use something similar to below: from loci. I wonder how it happened that ij. [ERROR] Exception during event handling: [Event] imagej. Open attached file Change view to 2nd plane Run adjust threshold Exception thrown: [ERROR] Exception during event handling: [Event] imagej. 0_322 [64-bit]; Windows 10 10. I manually set up a batch over a couple of files in a folder. 9. The proposed folder was the “5. java:456) May 17, 2024 · It’s approx 4. SwingSdiImageDisplay@48c4fedd Mar 17, 2019 · Installation of pyimagej has been discussed on the image. le Jun 25, 2018 · Warning: Some users have encountered incompatibility with ImageJ versions higher than 1. Sometimes there are additional information in the exception window (e. every time I try to start the app, I get this: can any one help me Apr 29, 2011 · Load an image. jar file and import it in Fiji… Dec 14, 2021 · Greetings! Fiji with ImageJ 1. sc Forum Loading Apr 5, 2017 · With ImageJ closed, go to the plugins folder of your imagej/Fiji install. assign. 52q20) with the same result. py:219: Cryptogr Mar 26, 2018 · Probably some strange dependency of one of my projects somewhere. xlsx”. olympus Mar 27, 2020 · Unzip and place the JAR file in the plugins folder of Fiji or ImageJ software to make the "SME Stacking" plugin available from the Fiji/ImageJ Plugins menu. exe) will generate a new ImageJ. Dataset field imagej. formats import ImageReader from loci. Would you know how to force imagej to continue taking reading from a list of images, if reading/loading one of the images encounters an error? ImageJ stops the process when it encounters an error! – Feb 21, 2018 · Hey, I have written a macro and get an java. legacy. Instead I get an exception window with the following information: (Fiji Is Just) ImageJ 2. O popup window appears with the Jun 21, 2018 · Cheers, Lech (Fiji Is Just) ImageJ 2. input1 to java. C:\Users\userA\AppData\Local\anaconda3\envs\pyimagej\lib\site-packages\paramiko\transport. plugins. getting all updates from all other update sites before uploading stuff)? Thanks for contributing an answer to Stack Overflow! Please be sure to answer the question. Apr 19, 2016 · Thanks for contributing an answer to Stack Overflow! Please be sure to answer the question. target/imagej-troubleshooting-0. I didn't investigate the source code of this rather old plugin, but here is an ImageJ-macro that should do what you want (with some flickering): Aug 20, 2020 · Module Threw Exception [Error] - Image. init(mode='headless'). ui. ImageJ@45de530a consumed = false display = imagej. jre\bin\javaw. Jan 14, 2021 · If you are installing ImageJ on Windows, we strongly recommend that you store your ImageJ. Sep 26, 2011 · Milestone changed from imagej-2. 5kx4. NullPointerException - Usage & Issues Loading Apr 6, 2017 · Hello everybody, I am using windows 10 64 bit and I have java 8 installed. xlsx file that it is referencing is actually an excel spreadsheet that the plugin is supposed to automatically generate on the Desktop under its default name “Rename me after writing is done. safeMultiply32(DataTools. Oct 20, 2021 · Try setting the SITK_SHOW_COMMAND to point directly to the ImageJ executable. app/ImageJ-linux64, Fiji. After initialising the object, opening an image and converting the image to imageplus: image = ij. io. Aug 7, 2017 · I am having an issue with setting the threshold in batch mode. 0_172 [64-bit]; Windows 10 10. 41i and later, returns "<Error: message>" if there any error, including host or file not found. exe. SwingDisplayWindow. I’ve been trying to solve this problem for hours, trying everything I’ve seen on the internet, but nothing seems to work. plugin. @ctrueden and @hinerm both helped create this more minimal example of the crash. rst as noted by @Thrameos but it was unable to catch any meaningful traces. Can I somehow track down which lines the exception causes? I could not find anything regarding this; sorry if my search was not thorough enough. Exception: [ERROR] java. Some things to note with this version of the plugin: Jul 3, 2023 · Hello. File. 0; 6793MB of 190000MB (3%) java. cfg that uses the Java you just installed. Jan 31, 2022 · For the “filenotfound” exception, the . core. close(SwingDisplayPanel. Any help would be highly appreciated. exe-Xmx2048m -cp ij. Sep 6, 2018 · An IO (Input-Output) Exception is predictably caused by something wrong with your input or output. apple. Future versions of the plugin will be Sep 15, 2022 · I am still having this problem. sdi. May 11, 2023 · File Saving Error (IO Exception) - Development - Image. Now I want to include the Labkit segmentation as part of a macro that also does other stuff afterwards with additional files that are not being Jul 3, 2023 · Hello. http Jul 17, 2023 · 205 title = “ImageJ could not be initialized, due to the following error:” 206 exception_str = jstacktrace(exc) → 207 msg: JavaErrorMessageBox = JavaErrorMessageBox(title, exception_str) title = ‘ImageJ could not be initialized, due to the following error:’ exception_str = ‘’ Jul 28, 2020 · There are 2 separate update sites with Bio-Formats builds, the Java-8 site contains the official releases and is what I would recommend people use. CurveFitter. I keep Sep 8, 2021 · @Weiya_Fan please always disclose when cross-posting, so that others can follow the discussion as well. [ERROR] Uncaught exception in thread Thread[plugin thread,6,plugin thread group] java. 0_45 [64-bit]”. makeInitialParamsAndVariations(CurveFitter. in this topic. vsi file into Image J to quantify RNAscope images ( fluorescence images with an overlap of 3 layers). java:260) Oct 26, 2012 · I've been trying to build an image processing app using ParticleAnalyzer of ImageJ 1. I found article on SDN about compressing and decompressing options in Java. ROI Manager Jul 11, 2019 · This issue was not present when I run the macro with ImageJ 1. 1. Scaler. openSequence(path, options) - Opens the images in the specified directory as a stack. Firstly, whilst the posted version of the plugin may work for you if the files are copied into ImageJ properly, I might recommend that you download the most recent version using the imageJ updater as I described at the end of my Jan10 post and as detailed at the bottom of my user page: Jun 22, 2023 · Hi Community, I have trained a classifier in Labkit that I now want to use as part of a macro. 49v (I did not test the intermediate versions). So here is the deal, I've downlo Feb 7, 2023 · Wondering if this could be fixed? (Fiji Is Just) ImageJ 2. Jul 26, 2018 · Hello, I apologize in advance for such an elementary question but I am having a surprising amount of trouble getting SimpleITK to open ImageJ as a viewer. in import ImporterOptions from loci. These errors indicate a "version skew" between the software libraries in your ImageJ installation. cfg file, it reads. app to such a directory, modern versions of Windows will deny ImageJ write Thanks to Stein Rorvik, ImageJ looks for the preferences file ("IJ_Prefs. e. swing. sc forum, e. Feb 20, 2023 · Hi I am trying to run the DiameterJ Segment plugin using pyimagej. java:260) During startup IJ2 barfs an exception related to legacy initialization: [WARNING] Failed to instantiate IJ1. What is Sep 11, 2023 · You signed in with another tab or window. jar ended up in your db. open(PATH_1) imp = ij. Feb 5, 2018 · Herbie, I try something else: Instead of saveAs(“Tiff”,lien), I write saveAs(“Tiff”); As such, a dialog windows opened. It is an image of 16Mb in size. 5; 128MB of 7191MB (1%) java. Jan 18, 2012 · Add Z axis to Boats. Does not return until the command has finished executing. The version of ImageJ I am using is 1. NullPointerException at ij. http. Yes, that’s exactly the case, but if the macro is programmed correctly this shouldn’t happen, because all the images are processed successively and independent of each other. 5k image I’ve tried on various machines with installation and same result. Additionally, I have noticed that the other Batch function, such as Convert, do not work either. Would you know a way to solve this issue? I can replicate the problem and it seems as if the plugin needs to actually display the image which is not the case with batch processing. 51n; Java 1. 53t; Java 1. On top of that, the ImageJ status bar indicates that less than 1% of RAM is being used (18MB of 2048MB). py. UnknownFormatException: Unknown file Jun 9, 2021 · I have downloaded the code and saved it as a text file. Move the existing ‘Read_and_Write_Excel-1. ExecutionException: java. 13. ROI Manager But thanks to the ImageJ Legacy Bridge, most aspects of the original ImageJ work in headless mode, including via PyImageJ when initializing with imagej. IllegalStateException: Cannot add com. java. app/jars directory of your ImageJ installation; Start ImageJ I faced the same problem. display. Apr 20, 2023 · Hi all, I am trying to use the Batch Macro function in FIJI to open my multi-channel file and only save the brightfield channel so that I can draw around the cells and create ROIs for subsequent analysis. parseHTTPHeader(HttpClient. ZipFile was not able to handle but WinRar unpacked it just fine. fusion” folder. Also, there are currently a few open issues/PRs in scyjava (#5 and #7) and pyimagej (). the algorithm has been tested perfectly on my mac, but when I shipped the runnable jar onto the hadoop cluster, it kept throwing the awt headless exception. Uses a virtual stack if the 'options' string contains 'virtual'. 0_91 [64-bit]; Mac OS X 10. After it finishes “Extracting features”, which takes a few hours, I get a “NotEnoughDataPointsException”: mpicbg. NullPointerException at Jan 7, 2016 · Thanks for contributing an answer to Stack Overflow! Please be sure to answer the question. I am very new to using Image J. IllegalArgumentException: Pixel array is null at ij. Asking for help, clarification, or responding to other answers. 0. SocketException: Unexpected end of file from server at sun. I have then run the macro through going to Plugins > Macros > Run. This interface has access to all of the Java-based functions, and also has convenience functions for translating back and forth between the Python and Java environments. I get different results in batch mode ‘run(“Threshold…”, “Minimum”);’ (6 particles) than when I set the threshold “by hand” outside of batch mode (2 particles, the correct number). jar This JAR (Java Archive) file is the platform-independent core of ImageJ. im Aug 21, 2017 · You most likely just using up the ram allocated to ImageJ. ArrayIndexOutOfBoundsException every 20-30 images. getProcessor(ImageStack. That said, there are a couple of major areas of functionality in the original ImageJ that do not work headless, and therefore do not work headless via PyImageJ. [ERROR] Exception java. eawt. String You signed in with another tab or window. 11. at imagej. 53c Help → Update ImageJ… returns: Help → Update… returns the following in the console: [ERROR] Cannot connect to the Internet. 46 including Java. . [ERROR] Module threw exception java. AbstractData. plugins import BF from loci. models Oct 12, 2012 · Is there a way I can force ImageJ to continue with the process even though it encountered an error/exception? and report the filename maybe in the logs or another file? java error-handling May 29, 2013 · Open attached file Change view to 2nd plane Run adjust threshold Exception thrown: [ERROR] Exception during event handling: [Event] imagej. You switched accounts on another tab or window. I am very new to ImageJ/Fiji and need to analyze some stainings using the threshold method. java:927) at ij. UnsupportedOperationException. app") rather than in " C:\Program Files" or other system-wide directory. 0-rc-43/1. 0; 143MB of 24221MB (<1%) java. ImgIOException: loci. I am using “Translation” for the feature extraction model and the registration model. Checking the Java version. The Toolbar Menus macro demonstrates how to do this. To create a sequence in VirtualDub, use the File/Save image sequence command, set "Minimum number of digits in name" to 3 or more, and check "Windows BMP NOTICE! This is a static HTML version of a legacy ImageJ Trac ticket. I have “Shrinkage constrain” and “save transforms” checked. During startup IJ2 barfs an exception related to legacy initialization: [WARNING] Failed to instantiate IJ1. formats import MetadataTools from ij import IJ from loci. jar) to the ImageJ. init() function and yields a wrapped ImageJ2 gateway, the net. May 3, 2017 · I am trying to register a stack of ~11,000 images using Register Virtual Stack Slices (RVSS). imglib2. It can be thrown by most classes in the java. This is where the error occurs. However, while this runs fine: import imagej ij = imagej. You can tell which Java version ImageJ is using by clicking the ImageJ status bar and looking for the part that says e. common. 0-beta4 comment:4 Changed 2012-07-17T13:30:49-05:00 by bdezonia Description modified May 8, 2018 · When i check the imagej. setId(str(indivFile)) options Mar 7, 2012 · Exception (below) thrown repeatedly. JLayeredPane cannot be cast to imagej. MsMovedEvent context = imagej. IllegalArgumentException: Can not set imagej. With v1. It's seems that in the previous version (e. Exception below thrown: [ERROR] Exception during event handling: [Event] imagej. co. data. 4 Menu Tools You can use the newMenu function to add menus to the toolbar. Show(img, 'sample image', debugOn=True) On Linux systems, SimpleITK searches the path for the following options: Fiji. This File > Close (Cmd+W) doesn't completely close the display window and throws the following exception: [ERROR] Module threw exception java. ext. OK, here's my slightly modified version of your script: This gateway interface is activated using the imagej. 0_66 [64-bit]; Linux 4. txt") in the current directory, the ImageJ directory and the username/. DataTools. 8. If you move ImageJ. You signed out in another tab or window. However, when I try to convert my green slide from my RGB stack to an 8-bit version, the software throws this exception and prevents me from continuing the analysis. I have installed python on my Windows 7 work computer using Ana… Feb 1, 2024 · Hello, I use Fiji for image processing. event. (Fiji Is Just) ImageJ 2. One (or both) of the arrays must be shorter that that, which is why you are getting the exception. Aug 31, 2011 · The ImageJ project now uses GitHub Issues for issue tracking. ApplicationListener after installing an app event handler Aug 17, 2017 · That will show you the search path it's using to try and find ImageJ. ClassCastException: javax. NullPointerException at Hello everyone, An exception message appears when I try to open a particular tif file with ImageJ. exe or ij147-jdk6-setup. jar’ somewhere (incase you wish to reinstate it later). input. Ticket #733 (closed [ERROR] Module threw exception Another way to open an AVI movie in ImageJ is to use VirtualDub (Windows only) to convert it to an image sequence and then open the sequence using ImageJ's File/Import/Image Sequence command. 51a; Java 1. in import ImportProcess from loci. RuntimeException: Module threw exception at net. HttpClient. IllegalArgumentException: Array size too large: 63575 x 36874 x 1 at loci. formats Dec 7, 2021 · Hello all, If anybody can help me it would be really appreciated! I am running a macro where one of the lines is simply converting a big RGB stack to 8 bit color, it works fine for other files of the same kind, but for the one with longer frames I get the below exception error, if anyone can advise on why this happens and how to correct it please let me know, I really need to use the 8 bit The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others. This has been working perfectly, until today when this function is no longer working. String If there are no major alignment errors the average and maximal displacement will be below or around 1 pixel. I can use the plugin in IntelliJ, but when I am using Maven Package to build the . However the plugin ends up working just fine. util. ArrayIndexOutOfBoundsException: 414720. ImageJ. Exception followed by a random number) , sometimes just this one line. net. to_imageplus(image) I run the following co Aug 17, 2021 · Hi pyimagej folks, I was just trying to use a specific version of pyimagej, because according to the documentation, that makes my workflow reproducible. DatasetRestructuredEvent context = imagej. NullPointerException” any thoughts May 18, 2016 · They are all produced via ImageJ and in the same way. However, I really can’t find anywhere about how to solve this issue. java:949) at loci. I downloaded imageJ but I can not start it. That’s good practice in programming anyway. Debugging shows PixelRecorder has correct multidim coords. In case of troubles, we recommend to use the ImageJ version 1. 0-beta4 comment:4 Changed 2012-07-17T13:30:49-05:00 by bdezonia Description modified Next, we want to run this plugin in ImageJ and see what happens: On the command line, run mvn clean install from the imagej-troubleshooting directory, to build a . Aug 31, 2011 · File > Close (Cmd+W) doesn't completely close the display window and throws the following exception: [ERROR] Module threw exception java. xml. Reload to refresh your session. ArrayIndexOutOfBoundsException: 0 at ij. ImageStack. 0-rc-59/1. If i download the lates FIJI version, goto FIJI update and Labkit to there. exe is available at: Index of /ij/download Aug 7, 2019 · I want to write some code in Python that will be used for manipulating data in Fiji. 0/1. , " C:\Users\[your name]\ImageJ. yrqfrn ikzh yfdutq rmjwsy jgjqj gupttm tcsakb tsd wxe fmlb