public boolean beadCalibration3d() {
imp = IJ.getImage();
if (imp == null) {
IJ.noImage();
return false;
} else if (imp.getStackSize() == 1) {
IJ.error("Stack required");
return false;
} else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
// In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y);
// requires a Float.intBitsToFloat() conversion
IJ.error("8 or 16 bit greyscale image required");
return false;
}
width = imp.getWidth();
height = imp.getHeight();
nslices = imp.getStackSize();
imtitle = imp.getTitle();
models[0] = "*None*";
models[1] = "line";
models[2] = "2nd degree polynomial";
models[3] = "3rd degree polynomial";
models[4] = "4th degree polynomial";
GenericDialog gd = new GenericDialog("3D PALM calibration");
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
gd.addNumericField(
"Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
gd.addCheckbox(
"Show divergence of bead positions against model",
prefs.get("QuickPALM.3Dcal_showDivergence", false));
gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.pthrsh", pthrsh * 100);
cal_z = gd.getNextNumber();
prefs.set("QuickPALM.z-step", cal_z);
window = (int) gd.getNextNumber();
prefs.set("QuickPALM.window", window);
model = gd.getNextChoice();
prefs.set("QuickPALM.model", model);
part_divergence = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
part_extrainfo = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
return true;
}
public boolean reconstructDataset() {
view_modes[0] = "3D color";
view_modes[1] = "2D histogram";
view_modes[2] = "2D particle intensity (16-bit)";
view_modes[3] = "2D particle intensity (8-bit)";
GenericDialog gd = new GenericDialog("Reconstruct PALM/STORM Dataset");
gd.addNumericField(
"Target pixel size for the rendered image (nm)",
prefs.get("QuickPALM.viewer_tpixelsize", 30),
2);
gd.addNumericField("Original image width (px)", prefs.get("QuickPALM.viewer_owidth", 512), 2);
gd.addNumericField("Original image height (px)", prefs.get("QuickPALM.viewer_oheight", 512), 2);
gd.addChoice("View mode", view_modes, prefs.get("QuickPALM.view_mode", view_modes[1]));
// gd.addNumericField("Allow image saturation (%)", prefs.get("QuickPALM.saturation", 50), 0);
gd.addCheckbox(
"Simulate sub-difraction spot (gaussian convolution - only 2D)",
prefs.get("QuickPALM.viewer_doConvolve", true));
// gd.addCheckbox("Make 3D stack", prefs.get("QuickPALM.viewer_do3d", false));
// gd.addCheckbox("Make movie", prefs.get("QuickPALM.viewer_doMovie", false));
gd.addCheckbox("Make 3D stack", false);
gd.addCheckbox("Make movie", false);
// gd.addCheckbox("Save only and don't show", prefs.get("QuickPALM.viewer_doSave", false));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Simulate sub-difraction spot settings (used only if selected) --");
gd.addNumericField("FWHM of the spot", prefs.get("QuickPALM.viewer_fwhm", 30), 2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make 3D stack settings (used only if selected) --");
gd.addNumericField("Z-spacing between slices (nm)", prefs.get("QuickPALM.viewer_zstep", 50), 2);
gd.addNumericField(
"Merge particle Z-position above (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergeabove", 0),
2);
gd.addNumericField(
"Merge particle Z-position bellow (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergebellow", 0),
2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make movie settings (used only if selected) --");
gd.addNumericField(
"Make a reconstruction in every N frames", prefs.get("QuickPALM.viewer_update", 10), 0);
gd.addNumericField(
"Accumulate N neighboring frames for each reconstruction\n(set to 0 to accumulate all the preceding frames)",
prefs.get("QuickPALM.viewer_accumulate", 100),
0);
gd.showDialog();
if (gd.wasCanceled()) return false;
viewer_tpixelsize = gd.getNextNumber();
prefs.set("QuickPALM.viewer_tpixelsize", viewer_tpixelsize);
viewer_owidth = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_owidth", viewer_owidth);
viewer_oheight = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_oheight", viewer_oheight);
view_mode = gd.getNextChoice();
prefs.set("QuickPALM.view_mode", view_mode);
viewer_doConvolve = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doConvolve", viewer_doConvolve);
viewer_do3d = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_do3d", viewer_do3d);
viewer_doMovie = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doMovie", viewer_doMovie);
// viewer_doSave = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_doSave", viewer_doSave);
// -- Simulate sub-difraction spot
viewer_fwhm = gd.getNextNumber();
prefs.set("QuickPALM.viewer_fwhm", viewer_fwhm);
// -- Show B&W
// viewer_is8bit = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_is8bit", viewer_is8bit);
// -- Make 3D stack
viewer_zstep = gd.getNextNumber();
prefs.set("QuickPALM.viewer_zstep", viewer_zstep);
viewer_mergeabove = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergeabove", viewer_mergeabove);
viewer_mergebellow = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergebellow", viewer_mergebellow);
// -- Make Movie
viewer_update = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_update", viewer_update);
viewer_accumulate = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_accumulate", viewer_accumulate);
return true;
}