Hi Philippe, I tested this process on my Linux x64 system, and all works. However, I noticed that ThunderSTORM builds two different JAR files in the target folder: one called Thunder_STORM.jar and another called original-Thunder_STORM.jar.
The Thunder_STORM.jar is a so-called "uber-JAR" or "fat JAR" intended to collect all classes from all dependencies into a single JAR file. See https://imagej.net/develop/uber-jars for more details. The original-Thunder_STORM.jar is the originally constructed JAR file with only the ThunderSTORM classes, not all the dependencies lumped in. In my test, I moved all the JAR files from the target/dependency folder into a new `ImageJ/jars` folder, and placed *original-Thunder_STORM.jar* into `ImageJ/plugins`. I did not use the Thunder_STORM.jar uber-JAR. For completeness, I then tested the uber-JAR as well, deleting the entire `ImageJ/jars` folder with all the dependencies, and deleting the `ImageJ/plugins/original-Thunder_STORM.jar`, and instead placing the `Thunder_STORM.jar` into `ImageJ/plugins`. Then I ran the "Run analysis" plugin again on your data, and it worked just the same. So it looks like either way works: the single simple Thunder_STORM.jar, or the more granular dependency JARs plus original-Thunder_STORM.jar. I was however testing on Linux, not Windows. There may be platform-specific issues. Or there may be a bad interaction with some other plugin(s) you have installed. I was testing with a fresh ImageJ with no other extra plugins. If you still have trouble, please give more details including exactly what goes wrong, error message, etc. Regards, Curtis P.S. I notice you removed the mailing list from the thread. I have put it back on the list, since this discussion could interest others besides only yourself. On Wed, Apr 17, 2024 at 4:01 PM CARL Philippe (LBP) < [email protected]> wrote: > Dear Curtis, > I tried your proposed solution which generated a whole bunch of .jar files. > But when trying to launch the thunderSTORM plugin (for the given analysis) > the problem still wasn't solved. > Please find under the following link (711 Ko): > http://punias.free.fr/inputZStack_cam.tif > <https://urldefense.com/v3/__http://punias.free.fr/inputZStack_cam.tif__;!!Mak6IKo!LFJVUh3wT3NWcY-agsvAoZJcz8mn9SMRPwgNRdj-0S9__dZZYxklH7-SbEZUpfoMcddsEN0CIZLNifo7CLHG0NpQ9xw$> > the calibration file on which you can launch the calibration procedure > with by doing: > Plugins>ThunderSTORM>3D_calibration>Cylindrical_lens_calibration > and saving the calibration file somewhere. > Then you can use the same picture in order to perform a 3D reconstruction > with > Plugins>ThunderSTORM>Run_analysis > and select the "PSF: Elliptical Gaussian (3D astigmatism)" where you > indicate the obtained calibration file (.yaml) within the "Calibration > file" stringField. > You will then get an error message thay you won't have when running under > Fiji. > I thank you very much in advance for your time and help! > My best regards, > Philippe > ------------------------------ > *De: *"Curtis Rueden" <[email protected]> > *À: *"CARL Philippe, LBP" <[email protected]> > *Envoyé: *Mardi 16 Avril 2024 15:33:44 > *Objet: *Re: Mandatory use of Fiji > > Hi Philippe, > > > In fact I very unfortunately discovered empirically the ImageJ2 > dependancy > > of the ThunderSTORM plugin. > > Sorry, I don't understand what you mean. As I said in my last email, > ThunderSTORM does not depend on ImageJ2. > > > But within which environment (or how) can I launch your proposed (easy) > code > > below? > > If I understand your setup correctly, you should be able to put commands > like the following into your batch file: > > %~dp0\apache-maven-3.8.4\bin\mvn dependency:copy-dependencies > copy target\dependency\*.jar C:\path\to\ImageJ\jars > > where "C:\path\to\ImageJ" is the location of your ImageJ installation. > > Does that answer your question? > > Regards, > Curtis > > On Tue, Apr 16, 2024 at 3:24 PM CARL Philippe (LBP) < > [email protected]> wrote: > >> Hi Curtis, >> Thanks a lot for your answer. >> In fact I very unfortunately discovered empirically the ImageJ2 >> dependancy of the ThunderSTORM plugin. >> I really apologize for my very simple (and thus stupid) question. >> But within which environment (or how) can I launch your proposed (easy) >> code below? >> Up to now I was compiling the code using the following .bat file: >> SET JAVA_HOME=%~dp0\jdk1.8.0_202 >> cd %~dp0\thunderstorm-dev-2024-04-11-a >> %~dp0\apache-maven-3.8.4\bin\mvn package -Dmaven.test.skip=true & pause >> And I'm really not specialist (not to say really a beginner) of this kind >> of setups. >> My best regards, >> Philippe >> >> ----- Mail original ----- >> De: "Curtis Rueden" <[email protected]> >> À: "imagej" <[email protected]> >> Envoyé: Mardi 16 Avril 2024 14:42:42 >> Objet: Re: Mandatory use of Fiji >> >> Hi Philippe, >> >> According to `mvn dependency:list` on the thunderstorm source code, there >> are no dependencies on any ImageJ2 libraries. Therefore, you should be >> able >> to run the software with vanilla ImageJ. My suggestion for how to achieve >> this most easily is: >> >> git clone >> https://urldefense.com/v3/__https://github.com/zitmen/thunderstorm__;!!Mak6IKo!J8zAorFbrMZAqTXjTfANlXcWyqHlMH2zIM8bRP-O2TdONnhd1a0YJ45GepeJTa7TV5UJFGJ3JKO3KtcSkRCE9-0K6w4$ >> cd thunderstorm >> mvn dependency:copy-dependencies >> cp target/dependency/*.jar /path/to/ImageJ/jars >> >> And you will have the needed dependencies for the thunderstorm plugin. >> >> You will also need the thunderstorm JAR file itself, of course. If you >> want >> to build that from source, you can: >> >> mvn package >> cp target/ThunderSTORM*.jar /path/to/ImageJ/plugins >> >> Regards, >> Curtis >> >> On Tue, Apr 16, 2024 at 1:19 PM CARL Philippe (LBP) < >> [email protected]> wrote: >> >> > Dear all, >> > Is it mandatory to use Fiji (instead the vanilla version of ImageJ) when >> > using a plugin implementing the snakeyaml library ( >> > >> https://urldefense.com/v3/__https://mvnrepository.com/artifact/org.yaml/snakeyaml__;!!Mak6IKo!J8zAorFbrMZAqTXjTfANlXcWyqHlMH2zIM8bRP-O2TdONnhd1a0YJ45GepeJTa7TV5UJFGJ3JKO3KtcSkRCEbiMieTg$ >> ) like thunderSTORM ( >> > >> https://urldefense.com/v3/__https://zitmen.github.io/thunderstorm/)?__;!!Mak6IKo!J8zAorFbrMZAqTXjTfANlXcWyqHlMH2zIM8bRP-O2TdONnhd1a0YJ45GepeJTa7TV5UJFGJ3JKO3KtcSkRCEjN3m6SE$ >> > I thank you very much in advance for your lighting on this. >> > My best regards, >> > Philippe >> > >> > Philippe CARL >> > Laboratoire de Bioimagerie et Pathologies >> > UMR 7021 CNRS - Université de Strasbourg >> > Faculté de Pharmacie >> > 74 route du Rhin >> > 67401 ILLKIRCH >> > Tel : +33(0)3 68 85 41 41 >> > >> > -- >> > ImageJ mailing list: >> https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!Mak6IKo!J8zAorFbrMZAqTXjTfANlXcWyqHlMH2zIM8bRP-O2TdONnhd1a0YJ45GepeJTa7TV5UJFGJ3JKO3KtcSkRCE0il-Asw$ >> > >> >> -- >> ImageJ mailing list: >> https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!Mak6IKo!J8zAorFbrMZAqTXjTfANlXcWyqHlMH2zIM8bRP-O2TdONnhd1a0YJ45GepeJTa7TV5UJFGJ3JKO3KtcSkRCE0il-Asw$ >> > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
