Hello,
I want to use Bio-formats within an ImageJ2 plugin but I cannot get the plugin to recognise any formats other than tiff, jpeg etc. Any microscopy proprietary formats can’t be read. I’ve been struggling with what seems to be a basic problem for a while now so I would really appreciate anyone from the Bioformats or Image.net teams giving me a few pointers.
Thanks
David
This is the code I’m using
// create the ImageJ application context with all available services
final ImageJ ij = new ImageJ();
ij.launch(args);
ij.ui().showUI();
// ask the user for a file to open
final File file = ij.ui().chooseFile(null, "open");
if (file != null) {
// load the dataset
final Dataset dataset = ij.scifio().datasetIO().open(file.getPath());
// show the image
ij.ui().show(dataset);
}
This is the very long dependency list I’m using in my pom file:
<dependencies>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
</dependency>
<dependency>
<groupId>loci</groupId>
<artifactId>loci-common</artifactId>
<version>5.0.0-beta1</version>
</dependency>
<dependency>
<groupId>loci</groupId>
<artifactId>loci_plugins</artifactId>
<version>5.0.0-beta1</version>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
<version>6.1.1</version>
</dependency>
<dependency>
<groupId>loci</groupId>
<artifactId>loci-common</artifactId>
<version>5.0.0-beta1</version>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
<version>imagej-2.0.0-rc-69</version>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
</dependency>
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio</artifactId>
</dependency>
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio-ome-xml</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-common</artifactId>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>bioformats_package</artifactId>
<version>6.5.1</version>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
<version>6.1.1</version>
</dependency>
<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
<version>6.0.6</version>
</dependency>
<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-xml</artifactId>
<version>6.2.2</version>
</dependency>
</dependencies>
This is the error:
Exception in thread "main" java.io.IOException: io.scif.img.ImgIOException: io.scif.FormatException: C:\Users\coil\Desktop\Emoke\201209_L2_4_FalconFibers_IF_ChCID488_RbCENPC555_rCal1647_01_02_R3D_D3D_prj.dv: No supported format found.
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:135)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:110)
at coil.bio.ed.ac.uk.TestOpener.main(TestOpener.java:87)
Caused by: io.scif.img.ImgIOException: io.scif.FormatException: C:\Users\coil\Desktop\Emoke\201209_L2_4_FalconFibers_IF_ChCID488_RbCENPC555_rCal1647_01_02_R3D_D3D_prj.dv: No supported format found.
at io.scif.img.ImgOpener.createReader(ImgOpener.java:425)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:125)
... 2 more
Caused by: io.scif.FormatException: C:\Users\coil\Desktop\Emoke\201209_L2_4_FalconFibers_IF_ChCID488_RbCENPC555_rCal1647_01_02_R3D_D3D_prj.dv: No supported format found.
at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:350)
at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:316)
at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:88)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:419)
... 4 more