Merge pull request #3 from SBU-BMI/develop

Develop
SBU-BMI · Mar 11, 2019 · 9687a52 · 9687a52
2 parents 0ff05d1 + e3cb8e6
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Showing 6 changed files with 44 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -1 +1,8 @@
 # Nanoborb
+The [user guide screencast](https://drive.google.com/open?id=1HkkL5FqEIgi7fzqKijtUhWBPlplh_uHF) should explain the basics of Nanoborb.
+
+Installation Instructions
+
+Windows - 1) Download zip file. 2) Unzip. 3) Run "nanoborb.exe" in the unzipped folder
+
+MacOS - 1) Download zip file. 2) Unzip. 3) Move Nanoborb app to Applications folder. 4) Double-click copied Nanoborb file to run.
diff --git a/files/webfiles/about.html b/files/webfiles/about.html
diff --git a/files/webfiles/caMicroscope b/files/webfiles/caMicroscope
diff --git a/files/webfiles/debug/svs_demo.js b/files/webfiles/debug/svs_demo.js
@@ -23,7 +23,8 @@ fetch(p+"/info.json").then(response => {
             "profile": [ "http://iiif.io/api/image/2/level2.json" ],
             "protocol": "http://iiif.io/api/image",
             "tiles": [{
-              "scaleFactors": [ 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536, 131072, 262144],
+			  "scaleFactors": [ 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536, 131072, 262144],
+              //"scaleFactors": [ 1, 2, 4, 8, 16],
               "width": 256
             }]
         }

diff --git a/files/webfiles/splash.html b/files/webfiles/splash.html
@@ -5,15 +5,36 @@
 -->
 <html>
     <head>
-        <title>QuipLite</title>
+        <title>Nanoborb</title>
         <meta charset="UTF-8">
         <meta name="viewport" content="width=device-width, initial-scale=1.0">
     </head>
+    <style>
+        body {
+            background-color: #fdfdfd
+        }
+    </style>
     <body>
     <div id='img'><img src="./Nanoborb-256x256.png"/></div>
-        <div>Saltz, J., Sharma, A., Iyer, G., Bremer, E., Wang, F., Jasniewski, A., DiPrima, T., Almeida, J.S., Gao, Y., Zhao, T., et al. (2017). A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images. Cancer Res. 77, e79–e82.<br>
-
-caMicroscope — A Platform for Digital Pathology Data Management and Visualization <a href="http://camicroscope.org">http://camicroscope.org</a></div>
+    <strong>What is Nanoborb?</strong><br>
+    <p>Nanoborb is a desktop version of a subset of functions providing by the <a href="https://sbu-bmi.github.io/quip_distro/">QuIP Platform</a>.  With the current version of Nanoborb, you can perform
+    the following functions:</p>
+    <list>
+    <li>Load and view Whole Slide Images (WSI)</li>
+    <li>Mark-up and annotate these images</li>
+    <li>Save and reload these markups to a standard json file</li>
+    <li>View images side-by-side with image overlay markups.</li>
+    <li>Overlay computed heatmaps on images.</li>
+    <li>Get approximate counts of nuclei</li>
+    </list>
+
+    <p>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
+    <a href="http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/">http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/</a>
+    to download some sample images if you don't have some of your own.  For further instructions, please watch and enjoy the following tutorial <a href="https://youtu.be/Q_DEQbX3cO4" target="_blank">video</a>.
+    You can return to this page by selecting on the menu bar "About-->Main Page".</p>
+
+    <strong>Frequently Asked Questions</strong>
+    <p>Where can I download new versions of Nanoborb and for other platforms? <a href="https://github.com/SBU-BMI/Nanoborb/releases" target="_blank">https://github.com/SBU-BMI/Nanoborb/releases</a></p>
 </body>
 <style>
 #img.egg {

diff --git a/src/main/java/edu/stonybrook/bmi/nanoborb/MainFrame.java b/src/main/java/edu/stonybrook/bmi/nanoborb/MainFrame.java
@@ -75,6 +75,7 @@ public void stateHasChanged(org.cef.CefApp.CefAppState state) {
         setTitle("Nanoborb");
         CefSettings settings = new CefSettings();
         settings.windowless_rendering_enabled = useOSR;
+        settings.cache_path = "bcache";
         cefApp_ = CefApp.getInstance(settings);
         client_ = cefApp_.createClient();
         downloadDialog downloadDialog = new downloadDialog(this);
@@ -164,10 +165,17 @@ public void actionPerformed(ActionEvent ae) {
         JMenuItem quipMenuItem = new JMenuItem(new AbstractAction("QuIP") {
             @Override
             public void actionPerformed(ActionEvent ae) {
-                browser_.loadURL("http://localhost:8888/files/about.html");
+                browser_.loadURL("https://sbu-bmi.github.io/quip_distro/");
             }
         });
         aboutMenu.add(quipMenuItem);
+        JMenuItem aboutMenuItem = new JMenuItem(new AbstractAction("Main Page") {
+            @Override
+            public void actionPerformed(ActionEvent ae) {
+                browser_.loadURL("http://localhost:8888/files/splash.html");
+            }
+        });
+        aboutMenu.add(aboutMenuItem);
         final JMenuItem showDevTools = new JMenuItem("Developer Tools");
         showDevTools.addActionListener((ActionEvent e) -> {
             Frame owner_ = this;