mstritt / orbit-image-analysis Goto Github PK

Hi,

I am trying to run the script for glomeruli segmentation.
I have however a few requests:

1. can I upload directly a tif image as input to the model? Could you show me the command to do so directly in the script?
2. Whenever I launch the command
   Session s = DLSegment.buildSession("models/20180202_glomeruli_detection_noquant.pb")
   orbit crashes and closes the whole application. I am using a Mac. What am I doing wrong? Is there something I am supposed to have installed that I forgot?

Sorry if my questions are naive, but is the first time I am using it. If you could do an example of your script, in which you show how to do it uploading directly a tif image and then launching the glomeruli detection script would be great.

Thanks!
Gio

Dear Sir or Madam,
the latest orbit version seems to have problems accessing my omero server, where the latest omero version (5.14.0) is installed.
I have tried the ports 4064 and 4063 with and without encryption, the connection test works and it shows that the user or password are wrong. In the web, there is a similar problem mentioned for older orbit versions. Therefore I think that it could be a problem with the omero and orbit version?
Wiht kind regards

Hi Manuel,

I want to train your resnet glomeruli segmentation model on the dataset of mice with the segmentation you provided with the article.
The segmentation are in the db file format, but to run the segmentation model, I need to export them into png to save them then in the mask folders, as you show in the deep learning scripts.
Could you provide with the script needed to export the annotations in the relevant format for the masks, to then run the relative deep learning scripts?

Thanks
Giovanna

OS: Ubuntu 18.04
Java: 11.0.6
Gradle: 6.2.2

Build:

$ cd orbit-image-analysis
$ ~/Downloads/gradle-6.2.2/bin/gradle jar

Configuration on demand is an incubating feature.

BUILD SUCCESSFUL in 520ms
4 actionable tasks: 4 up-to-date

Run:

$ java -XX:MaxPermSize=150m -Djavax.xml.parsers.DocumentBuilderFactory=com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl -cp "build/libs/orbit-image-analysis.jar;build/libs/lib/*" com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis

OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
Error: Could not find or load main class com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis
Caused by: java.lang.ClassNotFoundException: com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis

Hi Manuel,

would it be possible to have one sample image to test your segmentation script?

Thanks

Giovanna

d:\Eclipse\EclipseWorkSpace\orbit-image-analysis>java -XX:MaxPermSize=150m -Djavax.xml.parsers.DocumentBuilderFactory=com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl -cp "build/libs/orbit-image-analysis-3.08.jar;build/libs/lib/*" com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=150m; support was removed in 8.0
错误: 找不到或无法加载主类 com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis

The above is the error running log.I would be grateful if there could be a big god to help me solve it!!!

Hi Manuel,

I just saw that the TileMode is set to false by default. If I am not wrong, this will cause Orbit to load the whole Image into memory and not using Tile. Is there an advantage when TileMode is set to true?

Best, Tony

Hi Manuel

I were able to build the program with Gradle. But when I run it using the command you given, it shows me this error. Do you know what I have to change?

Best,
Tony
C:\Users\test\eclipse-workspace\orbit-image-analysis-3.08>java -XX:MaxPermSize=150m -Djavax.xml.parsers.DocumentBuilderFactory=com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl -cp "build/libs/orbit-image-analysis-3.08.jar;build/libs/lib/*" com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis
Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
02:44:36,418 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
02:44:36,419 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
02:44:36,420 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Users/test/eclipse-workspace/orbit-image-analysis-3.08/build/libs/orbit-image-analysis-3.08.jar!/logback.xml]
02:44:36,421 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
02:44:36,421 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/test/eclipse-workspace/orbit-image-analysis-3.08/build/libs/orbit-image-analysis-3.08.jar!/logback.xml]
02:44:36,421 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/Users/test/eclipse-workspace/orbit-image-analysis-3.08/build/libs/lib/image-provider-omero-1.5.10.jar!/logback.xml]
02:44:36,437 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@1ddf84b8 - URL [jar:file:/C:/Users/test/eclipse-workspace/orbit-image-analysis-3.08/build/libs/orbit-image-analysis-3.08.jar!/logback.xml] is not of type file
02:44:36,530 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
02:44:36,539 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
02:44:36,544 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [STDOUT]
02:44:36,553 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
02:44:36,604 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [com.actelion.research.orbit.imageAnalysis.utils.OrbitLogAppender]
02:44:36,604 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [Orbit]
02:44:36,606 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
02:44:36,607 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [com.actelion.research] to INFO
02:44:36,607 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to WARN
02:44:36,607 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [STDOUT] to Logger[ROOT]
02:44:36,608 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [Orbit] to Logger[ROOT]
02:44:36,608 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
02:44:36,609 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1139b2f3 - Registering current configuration as safe fallback point

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at org.pushingpixels.substance.internal.utils.SubstanceColorUtilities.getDefaultBackgroundColor(SubstanceColorUtilities.java:759)
at org.pushingpixels.substance.internal.utils.SubstanceColorUtilities.getBackgroundFillColor(SubstanceColorUtilities.java:661)
at org.pushingpixels.substance.internal.ui.SubstancePanelUI.__org__pushingpixels__substance__internal__ui__SubstancePanelUI__installDefaults(SubstancePanelUI.java:74)
at org.pushingpixels.substance.internal.ui.SubstancePanelUI.installDefaults(SubstancePanelUI.java)
at java.desktop/javax.swing.plaf.basic.BasicPanelUI.installUI(BasicPanelUI.java:62)
at org.pushingpixels.substance.internal.ui.SubstancePanelUI.__org__pushingpixels__substance__internal__ui__SubstancePanelUI__installUI(SubstancePanelUI.java)
at org.pushingpixels.substance.internal.ui.SubstancePanelUI.installUI(SubstancePanelUI.java)
at java.desktop/javax.swing.JComponent.setUI(JComponent.java:685)
at java.desktop/javax.swing.JPanel.setUI(JPanel.java:150)
at java.desktop/javax.swing.JPanel.updateUI(JPanel.java:126)
at java.desktop/javax.swing.JPanel.(JPanel.java:86)
at java.desktop/javax.swing.JPanel.(JPanel.java:109)
at java.desktop/javax.swing.JPanel.(JPanel.java:117)
at java.desktop/javax.swing.JRootPane.createGlassPane(JRootPane.java:521)
at java.desktop/javax.swing.JRootPane.(JRootPane.java:348)
at org.pushingpixels.flamingo.internal.ui.ribbon.JRibbonRootPane.(JRibbonRootPane.java:55)
at org.pushingpixels.flamingo.api.ribbon.JRibbonFrame.createRootPane(JRibbonFrame.java:552)
at java.desktop/javax.swing.JFrame.frameInit(JFrame.java:258)
at java.desktop/javax.swing.JFrame.(JFrame.java:181)
at org.pushingpixels.flamingo.api.ribbon.JRibbonFrame.(JRibbonFrame.java:285)
at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.(OrbitImageAnalysis.java:251)
at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.getInstance(OrbitImageAnalysis.java:2857)
at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis$15.run(OrbitImageAnalysis.java:2965)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Hi Manuel,

I have downaloded the public available repository with the mice images and annotations.
However I have a problem in uploading the annotations.
The annotations are in the orbit.db file which you realeased.
In the readme file it says it can be placed in the user-home to be automatically detected by the software.
I have installed locally orbit, created a folder where there is the orbit.db file, one image. But when I open it with orbit, I see the image, but no annotation.
How can I upload the orbit.db file?
Thanks
Giovanna

Hi Orbit Team,

When I am working with big Image (100MB jpg), the program takes up a mount of memory when the image is loaded. But afterwards, The amount of memory used keeped increasing up to 5GB, even when you are not doing anything. I think memory usage is accelerated when you move around the image.

Could you have a look into it please.

Thanks,
Tony Nguyen

hi,
trying to run orbit v363 on debian10.

installed to /opt/orbit

$> /opt/orbit/orbit.sh

launches the orbit gui but i get this message:

The complete startup log:

$> /opt/orbit/orbit.sh                                    
17:39:48,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
17:39:48,657 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
17:39:48,658 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml]
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/opt/orbit/lib/orbit-image-analysis.jar!/logback.xml]
17:39:48,658 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml]
17:39:48,675 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@6236eb5f - URL [jar:file:/opt/orbit/lib/image-provider-omero-1.7.2.jar!/logback.xml] is not of type file
17:39:48,745 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.apache] to WARN
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [httpclient] to WARN
17:39:48,754 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
17:39:48,755 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7c1e2a9e - Registering current configuration as safe fallback point

java.lang.IllegalArgumentException: wrong number of arguments
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at com.actelion.research.orbit.imageAnalysis.dal.DALConfig.<clinit>(DALConfig.java:79)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.getInfoString(OrbitImageAnalysis.java:794)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.<init>(OrbitImageAnalysis.java:281)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.getInstance(OrbitImageAnalysis.java:2782)
	at com.actelion.research.orbit.imageAnalysis.components.OrbitImageAnalysis.lambda$initSingleApplication$7(OrbitImageAnalysis.java:2864)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
	at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)
Orbit Image Analysis Version  3.63
Copyright (c) 2009-2020, Idorsia Pharmaceuticals Ltd. under GPLv3 license.
Developed by Manuel Stritt and Jonathan Fuller.

Login User: guest
Available temporary disk space: 8698 MB.
Tile memory size (Read): 0 tiles
Tile memory capacity (Write): 788 MB
Tile temp directory: /tmp
JVM Memory used/total: 248 / 3940 MB
Available Cores: 8
JVM version: 11.0.7+10
Lib directory: /opt/orbit/lib
Loaded model: none

Optional parameters: [.orbit|image file(.jpg,.tif,.bmp,.png,.gif,.svs)|url|rdf id  ]
use -noErrorPopups to get rid of error popups (can be useful if you have no network connection)

use --hideQuickSearch to hide the left search bar (can be useful if you have no network connection)

And my ~/OrbitOmero.properties:

#Orbit Omero Config
OmeroHost=undisclosed.server.domain
SearchLimit=1000
UseSSL=false
OmeroPort=4064
OmeroWebPort=80

Any help would be appreciated.

I find that Orbit runs really slowly on my computer. It's my laptop for work, so it doesn't have anything fancy like a SSD or a ton of RAM. It still works... but painfully slowly. If you could post recommended system requirements somewhere, I think it would be very helpful, just so I could have an idea of what to look for in my next computer (whenever that opportunity comes around... likely never, but hey, I can dream)

Hi Orbit team,

When I have a big image (100MB, 11'000 x 11'000 pixels), moving around within image is kind of slow. Could you have a look into it?

Many thanks.
Tony Nguyen

"I’m using Orbit in stand-alone mode. I’ve created and saved a model yesterday using several images. When I reopened the model today and tried to restore the training shapes, nothing happened. I didn’t move or rename the images, although this shouldn’t matter like you said."

See details here: https://forum.image.sc/t/create-a-classification-model-using-multiple-images/38762/3

Full details here: https://forum.image.sc/t/technical-problems-with-f3-command-orbit/32067

Proposal to limit the size of the dialog.

Dear Manuel and Jon,

I have been able to let your deep learning for glomeruli segmentation run. However I have a question concerning the training set you have used, considering what is written in the article (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007313).
In the section Segmentation (page 13-14/19 of the article) you talk about a way of variating the tiles, which I don't fully get.
Could you please explain better how you obtain those variants?
Also running all of your scripts exactly (with rotations and so on) I get 108773 tiles, while in the article you state that you obtained 87213 tiles.
Could you tell me more about this?

Thanks!
Giovanna

Hi! I'm trying to run a script from https://www.orbit.bio/deep-learning-models/ in command line:

$ groovy -cp "build/libs/orbit-image-analysis-3.64.jar:build/libs/lib/*" src/main/groovy/com/actelion/research/orbit/imageAnalysis/scripts/deepLearning/DeepLearningSegmentation.groovy 

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.vmplugin.v7.Java7$1 (file:/home/dkurt/orbit-image-analysis/build/libs/lib/groovy-2.5.7.jar) to constructor java.lang.invoke.MethodHandles$Lookup(java.lang.Class,int)
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.vmplugin.v7.Java7$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2021-01-25 20:11:58.168786: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-01-25 20:11:58.192078: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 4008000000 Hz
2021-01-25 20:11:58.192452: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fe029b82c40 executing computations on platform Host. Devices:
2021-01-25 20:11:58.192477: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
using Tensorflow 1.14.0
20:11:58.444 INFO  c.a.r.o.i.dal.DALConfig:230 - using config file: resources/config.properties 
20:11:58.448 INFO  c.a.r.o.i.dal.DALConfig:74 - Configured image provider: com.actelion.research.orbit.imageprovider.ImageProviderOmero
20:11:58.448 INFO  c.a.r.o.i.dal.DALConfig:75 - Different image providers can be configured in resources/config.properties or resources/config_custom.properties (priority).
20:11:58.466 INFO  c.a.r.o.i.ImageProviderOmero:133 - searching for OrbitOmero.properties in current directory (/home/dkurt/orbit-image-analysis)
20:11:58.478 INFO  c.a.r.o.i.ImageProviderOmero:143 - searching for OrbitOmero.properties in user home (/home/dkurt)
20:11:58.488 INFO  c.a.r.o.i.ImageProviderOmero:176 - Omero host: localhost
20:11:58.490 INFO  c.a.r.o.i.ImageProviderOmero:177 - Omero port: 4064
20:11:58.490 INFO  c.a.r.o.i.ImageProviderOmero:178 - Omero web port: 443
20:11:58.491 INFO  c.a.r.o.i.ImageProviderOmero:179 - Omero use SSL: false
20:11:58.491 INFO  c.a.r.o.i.ImageProviderOmero:180 - Omero use WebSockets: false
20:11:58.491 INFO  c.a.r.o.i.ImageProviderOmero:181 - Search limit: 1000
20:11:58.491 INFO  c.a.r.o.i.ImageProviderOmero:182 - Omero User Scaleout: 
20:11:58.503 WARN  c.a.r.o.i.dal.DALConfig:85 - Orbit will continue with the fallback local filesystem image provider.
20:11:58.507 INFO  c.a.r.o.i.dal.DALConfig:104 - scaleout mode: true
20:11:58.509 INFO  c.a.r.o.i.dal.DALConfig:152 - image provider: com.actelion.research.orbit.imageAnalysis.dal.ImageProviderLocal@7c2312fa
20:11:58.510 INFO  c.a.r.o.i.dal.DALConfig:153 - scaleOut: com.actelion.research.orbit.imageAnalysis.dal.ScaleoutNoop@4cb0a000
20:11:58.511 INFO  c.a.r.o.i.dal.DALConfig:169 - local db file: /home/dkurt/orbit.db
Caught: java.lang.NullPointerException
java.lang.NullPointerException
        at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:87)
        at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment.generateSegmentationAnnotations(DLSegment.java:78)
        at com.actelion.research.orbit.imageAnalysis.deeplearning.DLSegment$generateSegmentationAnnotations$0.call(Unknown Source)
        at DeepLearningSegmentation.run(DeepLearningSegmentation.groovy:50)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

orbit.db exists (downloaded from https://doi.org/10.5061/dryad.fqz612jpc). But there is an error at the following line because rdf is null:

/cc @mstritt

https://forum.image.sc/t/rotate-an-image-in-orbit/33020

image is dimmed sometimes, see pdf for details
Troubleshootin dimness issue.pdf