Stitching big field of view

[olatarkowska]

Hello,

I am trying to stitch big field of view, tiles are comming from PerkinElmer high content screen microscope. I was trying to use BigStitcher but looks like registration process is not aligning tiles quit right. They are all placed in one location

Could anyone advice about using BigStitcher in immunofluorescent images?

Thanks
Ola

[bogovicj (John Bogovic)]

Hi @olatarkowska,

Welcome to the forum.

I’ve run into problems like this when BigStitcher doesn’t have a good starting point.

Do you have approximate locations of the tiles (maybe from image metadata)? And do you know
if BigStitcher is aware of these approximate positions?

Also, do you know the approximate overlap of the tiles?

John

[olatarkowska]

Hi @bogovicj,

Thank you for your quick reply,m. My dataset is PerkinElmer Harmony, it contains all of the coordinates in xml metadata associated with 2D planes. Bigstitcher is able to read metadata as BioFormats (cc: @s.besson) fully supports Harmony but for some reason it is not aligning them right and seems to not pickinig up correct coordinates from metadata. Am I doing something wrong?

Ola

[olatarkowska]

Maybe @StephanPreibisch could comment and help?

Ola

[John_Xu]

I found this one to be useful

PerkinElmer Operetta CLS Importer And Groovy Parallelization

Dear Forum We finished the release of a little piece of code in order to recreate hyperstacks from a list of TIFF files exported from a PerkinElmer Operetta CLS You can find the file, information and dependencies here, we will add a page on the ImageJ Wiki soon https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/perkinelmer-stitching/ While it is rather boring on its own, the nice thing was to play around with Parallelization in Groovy usin…

Cheers,
John

[William]

Hi,

I installed in Fiji the Operetta Importer plugin, which runs regularly. When I try to process some wells of a plate the code creates the requested images, but if I select wells separated by a gap into the plate (wells not acquired) I get the following error message:

[ERROR] org.scijava.module.MethodCallException: Error executing method: ch.epfl.biop.operetta.commands.OperettaImporter#doProcess
at org.scijava.module.MethodRef.execute(MethodRef.java:74)
at org.scijava.module.AbstractModuleItem.callback(AbstractModuleItem.java:230)
at org.scijava.widget.DefaultWidgetModel.callback(DefaultWidgetModel.java:183)
at org.scijava.ui.swing.widget.SwingButtonWidget$1.actionPerformed(SwingButtonWidget.java:83)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.module.MethodRef.execute(MethodRef.java:70)
… 39 more
Caused by: java.util.NoSuchElementException: No value present
at java.util.Optional.get(Optional.java:135)
at ch.epfl.biop.operetta.OperettaManager.getWell(OperettaManager.java:321)
at ch.epfl.biop.operetta.commands.OperettaImporter.lambda$doProcess$1(OperettaImporter.java:335)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at ch.epfl.biop.operetta.commands.OperettaImporter.doProcess(OperettaImporter.java:336)
… 44 more
[ERROR] org.scijava.module.MethodCallException: Error executing method: ch.epfl.biop.operetta.commands.OperettaImporter#doProcess
at org.scijava.module.MethodRef.execute(MethodRef.java:74)
at org.scijava.module.AbstractModuleItem.callback(AbstractModuleItem.java:230)
at org.scijava.widget.DefaultWidgetModel.callback(DefaultWidgetModel.java:183)
at org.scijava.ui.swing.widget.SwingButtonWidget$1.actionPerformed(SwingButtonWidget.java:83)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.module.MethodRef.execute(MethodRef.java:70)
… 39 more
Caused by: java.util.NoSuchElementException: No value present
at java.util.Optional.get(Optional.java:135)
at ch.epfl.biop.operetta.OperettaManager.getWell(OperettaManager.java:321)
at ch.epfl.biop.operetta.commands.OperettaImporter.lambda$doProcess$1(OperettaImporter.java:335)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at ch.epfl.biop.operetta.commands.OperettaImporter.doProcess(OperettaImporter.java:336)
… 44 more

Can you help me?

Thank you in advance.

Regards,

William