Can not select gate

[gabrielpan147]

Hello, I tried to process some images but I can not select gate. Here is the error log:

[ERROR] org.scijava.module.MethodCallException: Error executing method: de.embl.cba.cellview.command.CellViewProcessorCommand#selectGateButtonCallback at org.scijava.module.MethodRef.execute(MethodRef.java:71) at org.scijava.module.AbstractModuleItem.callback(AbstractModuleItem.java:227) at org.scijava.widget.DefaultWidgetModel.callback(DefaultWidgetModel.java:179) at org.scijava.ui.swing.widget.SwingButtonWidget$1.actionPerformed(SwingButtonWidget.java:82) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$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.GeneratedMethodAccessor23.invoke(Unknown Source) 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:67) ... 39 more Caused by: java.lang.NullPointerException at de.embl.cba.cellview.command.CellViewProcessorCommand.selectGateButtonCallback(CellViewProcessorCommand.java:265) ... 43 more

[schraivo]

Can you share an example dataset (e.g. FCS file plus a few images)?

[tischi]

@gabrielpan147 thank you for getting in touch!

As @schraivo pointed out a minimal example data set and an short description on when you clicked where (in which order) would be needed to debug this.

[gabrielpan147]

Thank you for your reply! I have attached some of my demo data here. I try to mimic your data structure. since there is not a step by step instruction, I am not sure if I followed the correct data structure or miss any files. Please take a look and correct me if I'm wrong. Thanks in advance!

demo.zip

[tischi]

Thank you @gabrielpan147 ! And you are raising a good point here!

@schraivo if you have time, could you please also provide a minimal dataset?

We should definitely add something for download to the README!

[schraivo]

Sorry for the delay, I've been on vacation (and sick afterwards). Here's a small dataset:

pmaxGFP_small.zip

[tischi]

@schraivo

Your reduced_gated table contains " " surrounding each line. This leads to an error when parsing the table. I could invest time to change the code to handle this, but this is very non-standard, it would be better if you change your way of creating the table such that it does not contain the ".

"path   Cells   Single Cells    DRAQ7 neg   GFP pos"
"../images/00000000/HeLa RIEN pmaxGFP_00000000.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000001.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000002.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000003.tiff TRUE    TRUE    TRUE    FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000004.tiff TRUE    TRUE    TRUE    FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000005.tiff TRUE    TRUE    TRUE    FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000006.tiff TRUE    TRUE    TRUE    TRUE"
"../images/00000000/HeLa RIEN pmaxGFP_00000007.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000008.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000009.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000010.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000011.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000012.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000013.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000014.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000015.tiff TRUE    TRUE    TRUE    FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000016.tiff TRUE    TRUE    TRUE    TRUE"
"../images/00000000/HeLa RIEN pmaxGFP_00000017.tiff FALSE   FALSE   FALSE   FALSE"
"../images/00000000/HeLa RIEN pmaxGFP_00000018.tiff FALSE   FALSE   FALSE   FALSE"

---

@gabrielpan147 in your case the countpath.csv table in principle works, but I had hard-coded in my code that the table must have more than 5 rows while yours only has 3 and thus it crashes. This is fixed now in the code, but not yet uploaded to Fiji.

Do you have a table with more rows to test with?

1. Open the table with Add files….
2. Select the table and gate using Select gate

[schraivo]

Tischi, can you use the following dataset? /g/bdimsort/testdata/pmaxGFP_small

[gabrielpan147]

Hi Tischi,

Thank you for your testing! It is very interesting that the gating only works with more than 5 rows. Yes I have a larger test dataset, I will try it soon and let you know the result.

Thanks again!! Gabriel

[gabrielpan147]

BTW, when using the plugins, is there a way to determine a scale bar of the image?

[schraivo]

BTW, when using the plugins, is there a way to determine a scale bar of the image?

The scale bar can't be added within the tool. We didn't add this option since the scale bar is actually easier to add retrospectively (every image from ICS is 60 µm wide). The exception is when cropping images during image processing with our Fiji plugin (see the cropping option in our Fiji plugin), you need to know how many pixels you cropped left and right.

[gabrielpan147]

BTW, when using the plugins, is there a way to determine a scale bar of the image?

The scale bar can't be added within the tool. We didn't add this option since the scale bar is actually easier to add retrospectively (every image from ICS is 60 µm wide). The exception is when cropping images during image processing with our Fiji plugin (see the cropping option in our Fiji plugin), you need to know how many pixels you cropped left and right.

Thank you and happy New Year! Do you have any references that can cite the width of the ICS image? I did not find anything from their technical specifications.

[schraivo]

Yes, you can cite our science paper, we described it in that paper.On Jan 2, 2024, at 06:55, Gabriel PAN @.***> wrote:

BTW, when using the plugins, is there a way to determine a scale bar of the image?

The scale bar can't be added within the tool. We didn't add this option since the scale bar is actually easier to add retrospectively (every image from ICS is 60 µm wide). The exception is when cropping images during image processing with our Fiji plugin (see the cropping option in our Fiji plugin), you need to know how many pixels you cropped left and right.

Thank you and happy New Year! Do you have any references that can cite the width of the ICS image? I did not find anything from their technical specifications.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

[tischi]

@gabrielpan147 can we close this issue?

[gabrielpan147]

@tischi yes sure, thank you again for your help!