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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see annotationList = new ArrayList(listModel.size());
for (int i = 0; i < listModel.getSize(); i++) {
SpotAnnotation annotation = (SpotAnnotation) listModel.get(i);
annotationList.add(annotation);
}
Collections.sort(annotationList, new Comparator() {
public int compare(SpotAnnotation o1, SpotAnnotation o2) {
if (useProposedClass)
return o1.getProposedClassNum() - o2.getProposedClassNum();
else return o1.getClassNum() - o2.getClassNum(); // real class
}
});
clear();
DefaultListModel newModel = new DefaultListModel();
for (SpotAnnotation annotation : annotationList) {
newModel.addElement(annotation);
}
list.setModel(newModel);
}
private void showHelp() {
final OrbitImageAnalysis oia = OrbitImageAnalysis.getInstance();
String color = OrbitUtils.DARKUI ? " color=white" : "";
String h = "" +
"Manual Classifiaction Module
" +
"Prerequisites
" +
"" +
"- Load or create (F4) an appropriate model (.cell)
" +
"- Load an image from Orbit
" +
"- Activate the manual classification module (Tools->Manuel Classification Module)
" +
"
" +
"Create a spot grid
" +
"" +
"- Select a region of interest (ROI) if you want. If you want to distrubute the grid over the whole image, continue with the next step.
" +
"- Click the 'Generate' button. Enter the number of spots you want to create and click 'ok'.
" +
"
" +
"Load existing spots
" +
"" +
"- Click on the 'Load' button to see if already detected spots have been persisted and load them.
" +
"
" +
"Quantify spot classes
" +
"" +
"- Click on 'Shuffle' to shuffle the list. This is necessary to achieve unbiased results. Generated spot lists are always shuffeled by default.
" +
"- Click on the first spot entry in the list.
" +
"- Use the keyboard and press a number (e.g. 1-3) to assign the selected spot a class.
The selection will automatically jump to the next spot. By holding down the ctrl key you can prevent this and the selection will stay on the selected item. " +
"- Use specific classes only when you are sure. Otherwise select the 'other' class. These spots will later be excluded from the statistics.
" +
"- With backspace you can make spots as unseen (undefined).
" +
"- Once you think you classified enough samples, click on 'Statistics' to retrieve a classification statistic.
" +
"- Click on 'Save' to persist your classifications. You can always continue with the classification by pressing the 'Load' button, shuffle your list and continue the classification.
" +
"
" +
"