diff --git a/README.md b/README.md index 2efcac2..a00282d 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,15 @@ # Nanoborb + +Since biomedical datasets and research motivation comes in different scales, it’s important that there exist tooling setups to fit these different needs. While in many situations, collaborative online research is helpful, we aim to provide visualization and analysis tools to individual users as well. + +NanoBorb is a offline-first toolkit for digitized whole slide images. By using NanoBorb, a user can interact fully with a large whole slide image without a powerful dedicated server, or even continuous internet access. Thus, users face minimal barriers to view, annotate, and analyze slides, as well as visualize and improve applicable machine learning methods. + +NanoBorb is built on ImageBox and caMicroscope. If a served version of the NanoBorb experience is desired, see quip distro. To provide feedback or suggestions click on the bug icon on pages where it appears. + + The [user guide screencast](https://drive.google.com/open?id=1HkkL5FqEIgi7fzqKijtUhWBPlplh_uHF) should explain the basics of Nanoborb. -Installation Instructions +## Installation Instructions Windows - 1) Download zip file. 2) Unzip. 3) Run "nanoborb.exe" in the unzipped folder diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml index 4d75c9a..feec114 100644 --- a/dependency-reduced-pom.xml +++ b/dependency-reduced-pom.xml @@ -3,7 +3,7 @@ 4.0.0 edu.stonybrook.bmi Nanoborb - 1.0 + 1.5.0 @@ -54,7 +54,7 @@ maven-surefire-plugin - 2.22.1 + 2.22.2 java.library.path diff --git a/files/webfiles/caMicroscope b/files/webfiles/caMicroscope index 77231db..feb09c2 160000 --- a/files/webfiles/caMicroscope +++ b/files/webfiles/caMicroscope @@ -1 +1 @@ -Subproject commit 77231db00f8f6648f51d38cb43cbc484158dab1f +Subproject commit feb09c243357ee494de0dd553498ba6d7a6f2e4b diff --git a/files/webfiles/splash.html b/files/webfiles/splash.html index 7731a1d..0bafc77 100644 --- a/files/webfiles/splash.html +++ b/files/webfiles/splash.html @@ -15,18 +15,11 @@ } -
+
Version 1.5.0
What is Nanoborb?
-

Nanoborb is a desktop version of a subset of functions providing by the QuIP Platform. With the current version of Nanoborb, you can perform - the following functions:

- -
  • Load and view Whole Slide Images (WSI)
    • -
  • Mark-up and annotate these images
    • -
  • Save and reload these markups to a standard json file
    • -
  • View images side-by-side with image overlay markups.
    • -
  • Overlay computed heatmaps on images.
    • -
  • Get approximate counts of nuclei
    • -     +

    Since biomedical datasets and research motivation comes in different scales, it’s important that there exist tooling setups to fit these different needs. While in many situations, collaborative online research is helpful, we aim to provide visualization and analysis tools to individual users as well.

    +

    NanoBorb is a offline-first toolkit for digitized whole slide images. By using NanoBorb, a user can interact fully with a large whole slide image without a powerful dedicated server, or even continuous internet access. Thus, users face minimal barriers to view, annotate, and analyze slides, as well as visualize and improve applicable machine learning methods.

    +

    NanoBorb is built on ImageBox and caMicroscope. If a served version of the NanoBorb experience is desired, see quip distro. To provide feedback or suggestions, click here or on the bug icon on pages where it appears.

    WSI images come in (unfortunately) a variety of formats such as Aperio SVS, BigTiff, and Olympus/CellSens VSI. To get you started, use the following link http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/ diff --git a/installjars.bat b/installjars.bat new file mode 100644 index 0000000..e99f6e3 --- /dev/null +++ b/installjars.bat @@ -0,0 +1,6 @@ +call mvn install:install-file -Dfile=ImageBox-1.1.1.jar -DgroupId=com.ebremer -DartifactId=ImageBox -Dversion=1.1.1 -Dpackaging=jar -DgeneratePom=true +call mvn install:install-file -Dfile=jcef.jar -DgroupId=jcef -DartifactId=jcef -Dversion=1.0 -Dpackaging=jar -DgeneratePom=true +call mvn install:install-file -Dfile=jogl-all.jar -DgroupId=jogl-all -DartifactId=jogl-all -Dversion=1.0 -Dpackaging=jar -DgeneratePom=true +call mvn install:install-file -Dfile=jogl-all-natives-windows-amd64.jar -DgroupId=jogl-all-natives-windows-amd64 -DartifactId=jogl-all-natives-windows-amd64 -Dversion=1.0 -Dpackaging=jar -DgeneratePom=true +call mvn install:install-file -Dfile=gluegen-rt.jar -DgroupId=gluegen-rt -DartifactId=gluegen-rt -Dversion=1.0 -Dpackaging=gluegen-rt -DgeneratePom=true +call mvn install:install-file -Dfile=gluegen-rt-natives-windows-amd64.jar -DgroupId=gluegen-rt-natives-windows-amd64 -DartifactId=gluegen-rt-natives-windows-amd64 -Dversion=1.0 -Dpackaging=jar -DgeneratePom=true \ No newline at end of file diff --git a/pom.xml b/pom.xml index a5ff224..87e3c35 100644 --- a/pom.xml +++ b/pom.xml @@ -1,110 +1,92 @@ - - - 4.0.0 - edu.stonybrook.bmi - Nanoborb - 1.0 - jar - - - jcef - jcef - 1.0 - - - jogl-all-natives-windows-amd64 - jogl-all-natives-windows-amd64 - 1.0 - - - jogl-all - jogl-all - 1.0 - - - gluegen-rt - gluegen-rt - 1.0 - - - gluegen-rt-natives-windows-amd64 - gluegen-rt-natives-windows-amd64 - 1.0 - - - com.ebremer - ImageBox - 1.0.5 - - - - UTF-8 - 1.8 - 1.8 - - - - - files/ - - **/*.js - **/*.html - **/*.svs - **/*.png - - - - - - org.apache.maven.plugins - maven-shade-plugin - 2.4.3 - - false - - - edu.stonybrook.bmi.nanoborb.MainFrame - - - - - false - - - - - *:* - - - META-INF/*.SF - META-INF/*.DSA - META-INF/*.RSA - - - - - - - package - - - shade - - - - - - maven-surefire-plugin - 2.22.1 - - - java.library.path - lib/win64 - - - - - + + + 4.0.0 + edu.stonybrook.bmi + Nanoborb + 1.5.0 + jar + + + com.ebremer + ImageBox + 1.1.1 + jar + + + jcef + jcef + 1.0 + jar + + + + UTF-8 + 1.8 + 1.8 + + + + + files/ + + **/*.js + **/*.html + **/*.svs + **/*.png + + + + + + org.apache.maven.plugins + maven-shade-plugin + 2.4.3 + + false + + + edu.stonybrook.bmi.nanoborb.MainFrame + + + + + false + + + + + *:* + + + META-INF/*.SF + META-INF/*.DSA + META-INF/*.RSA + + + + + + + package + + + shade + + + + + + maven-surefire-plugin + 2.22.2 + + + java.library.path + lib/win64 + + + + + \ No newline at end of file