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Fix image ROI reference population in Zeiss LSM and MIAS readers #4401

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Fix image ROI reference population in Zeiss LSM and MIAS readers #4401

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7ce103f
ZeissLSMReader: fix starting index when storing ROIRef for each series
sbesson Jan 16, 2026
7487006
MIASReader: fix starting index when storing ROIRef for each series
sbesson Jan 16, 2026
0a8f829
ZeissLSMReader: define transient roiRefIndex
sbesson Jan 20, 2026
89b85fd
MIASReader: initialize the roiRefIndex at the well level
sbesson Jan 20, 2026
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68 changes: 37 additions & 31 deletions components/formats-gpl/src/loci/formats/in/MIASReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -903,6 +903,7 @@ else if (name.endsWith("overlay.tif")) {
Color[] colors = new Color[getSizeC()];

int nextROI = 0;
int roiRefIndex = 0;
for (AnalysisFile af : analysisFiles) {
String file = af.filename;
String name = new Location(file).getName();
Expand All @@ -925,7 +926,8 @@ else if (name.endsWith("overlay.tif")) {

for (int j=start+1; j<lines.length; j++) {
populateROI(columnNames, lines[j].split("\t"), well,
nextROI++, position[1], position[2], store);
nextROI++, position[1], position[2], store, roiRefIndex);
roiRefIndex++;
}
}
else if (name.endsWith("AllModesOverlay.tif")) {
Expand All @@ -942,11 +944,15 @@ else if (name.endsWith("AllModesOverlay.tif")) {
store.setChannelColor(colors[position[3]], s, position[3]);
}
if (position[3] == 0) {
nextROI += parseMasks(store, well, nextROI, file);
int nOverlays = parseMasks(store, well, nextROI, file, roiRefIndex);
nextROI += nOverlays;
roiRefIndex += nOverlays;
}
}
else if (name.endsWith("overlay.tif")) {
nextROI += parseMasks(store, well, nextROI, file);
int nOverlays = parseMasks(store, well, nextROI, file, roiRefIndex);
nextROI += nOverlays;
roiRefIndex += nOverlays;
}
}
}
Expand Down Expand Up @@ -1029,24 +1035,24 @@ private int[] getPositionFromFile(String file) {
}

private void populateROI(List<String> columns, String[] data, int series,
int roi, int time, int z, MetadataStore store)
int roiIndex, int time, int z, MetadataStore store, int roiRefIndex)
{
String roiID = MetadataTools.createLSID("ROI", roi, 0);
store.setROIID(roiID, roi);
store.setImageROIRef(roiID, series, roi);
String roiID = MetadataTools.createLSID("ROI", roiIndex, 0);
store.setROIID(roiID, roiIndex);
store.setImageROIRef(roiID, series, roiRefIndex);

store.setEllipseID(MetadataTools.createLSID("Shape", roi, 0), roi, 0);
store.setEllipseTheT(new NonNegativeInteger(time), roi, 0);
store.setEllipseTheZ(new NonNegativeInteger(z), roi, 0);
store.setEllipseX(DataTools.parseDouble(data[columns.indexOf("Col")]), roi, 0);
store.setEllipseY(DataTools.parseDouble(data[columns.indexOf("Row")]), roi, 0);
store.setEllipseText(data[columns.indexOf("Label")], roi, 0);
store.setEllipseID(MetadataTools.createLSID("Shape", roiIndex, 0), roiIndex, 0);
store.setEllipseTheT(new NonNegativeInteger(time), roiIndex, 0);
store.setEllipseTheZ(new NonNegativeInteger(z), roiIndex, 0);
store.setEllipseX(DataTools.parseDouble(data[columns.indexOf("Col")]), roiIndex, 0);
store.setEllipseY(DataTools.parseDouble(data[columns.indexOf("Row")]), roiIndex, 0);
store.setEllipseText(data[columns.indexOf("Label")], roiIndex, 0);

double diam = Double.parseDouble(data[columns.indexOf("Cell Diam.")]);
double radius = diam / 2;

store.setEllipseRadiusX(radius, roi, 0);
store.setEllipseRadiusY(radius, roi, 0);
store.setEllipseRadiusX(radius, roiIndex, 0);
store.setEllipseRadiusY(radius, roiIndex, 0);

// NB: other attributes are "Nucleus Area", "Cell Type", and
// "Mean Nucleus Intens."
Expand Down Expand Up @@ -1164,7 +1170,7 @@ public void parseMasks(MetadataStore overlayStore)
int roi = 0;
parseMasks = true;
for (AnalysisFile roiFile : roiFiles) {
roi += parseMasks(overlayStore, roiFile.well, roi, roiFile.filename);
roi += parseMasks(overlayStore, roiFile.well, roi, roiFile.filename, 0);
}
parseMasks = originalMaskParsing;
}
Expand All @@ -1174,33 +1180,33 @@ public void parseMasks(MetadataStore overlayStore)
* MetadataStore.
* @return the number of masks parsed
*/
private int parseMasks(MetadataStore store, int series, int roi,
String overlayTiff) throws FormatException, IOException
private int parseMasks(MetadataStore store, int series, int roiIndex,
String overlayTiff, int roiRefIndex) throws FormatException, IOException
{
if (!parseMasks || series >= getSeriesCount()) return 0;
int nOverlays = 0;
for (int i=0; i<3; i++) {
String roiId = MetadataTools.createLSID("ROI", series, roi + nOverlays);
String roiId = MetadataTools.createLSID("ROI", series, roiIndex + nOverlays);
String maskId =
MetadataTools.createLSID("Mask", series, roi + nOverlays, 0);
MetadataTools.createLSID("Mask", series, roiIndex + nOverlays, 0);
overlayFiles.put(maskId, overlayTiff);
overlayPlanes.put(maskId, i);

boolean validMask = populateMaskPixels(series, roi + nOverlays, 0, store);
boolean validMask = populateMaskPixels(series, roiIndex + nOverlays, 0, store);
if (validMask) {
store.setROIID(roiId, roi + nOverlays);
store.setROIID(roiId, roiIndex + nOverlays);

String maskID = MetadataTools.createLSID("Shape", roi + nOverlays, 0);
store.setMaskID(maskID, roi + nOverlays, 0);
store.setMaskX(0d, roi + nOverlays, 0);
store.setMaskY(0d, roi + nOverlays, 0);
store.setMaskWidth((double) getSizeX(), roi + nOverlays, 0);
store.setMaskHeight((double) getSizeY(), roi + nOverlays, 0);
String maskID = MetadataTools.createLSID("Shape", roiIndex + nOverlays, 0);
store.setMaskID(maskID, roiIndex + nOverlays, 0);
store.setMaskX(0d, roiIndex + nOverlays, 0);
store.setMaskY(0d, roiIndex + nOverlays, 0);
store.setMaskWidth((double) getSizeX(), roiIndex + nOverlays, 0);
store.setMaskHeight((double) getSizeY(), roiIndex + nOverlays, 0);

int color = 0xff000000 | (0xff << (8 * (2 - i)));
store.setMaskStrokeColor(new Color(color), roi + nOverlays, 0);
store.setMaskFillColor(new Color(color), roi + nOverlays, 0);
store.setImageROIRef(roiId, series, roi + nOverlays);
store.setMaskStrokeColor(new Color(color), roiIndex + nOverlays, 0);
store.setMaskFillColor(new Color(color), roiIndex + nOverlays, 0);
store.setImageROIRef(roiId, series, roiRefIndex + nOverlays);
nOverlays++;
}
}
Expand Down
21 changes: 12 additions & 9 deletions components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,7 @@ public class ZeissLSMReader extends FormatReader {
private double originX, originY, originZ;

private int totalROIs = 0;
private transient int roiRefIndex;

private int prevPlane = -1;
private int prevChannel = 0;
Expand Down Expand Up @@ -973,6 +974,7 @@ else if (getSizeT() > 1) {

if (getMetadataOptions().getMetadataLevel() != MetadataLevel.NO_OVERLAYS)
{
roiRefIndex = 0;
for (int i=0; i<overlayOffsets.length; i++) {
parseOverlays(series, overlayOffsets[i], overlayKeys[i], store);
}
Expand Down Expand Up @@ -1614,6 +1616,7 @@ protected void parseOverlays(int series, long data, String suffix,

String roiID = MetadataTools.createLSID("ROI", i);
String shapeID = MetadataTools.createLSID("Shape", i, 0);
roiRefIndex++;

Length fontSize = FormatTools.getFontSize(fontHeight);
Length line = new Length(lineWidth, UNITS.PIXEL);
Expand All @@ -1632,7 +1635,7 @@ protected void parseOverlays(int series, long data, String suffix,
store.setLabelFontSize(fontSize, i, 0);
}
store.setLabelStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case LINE:
Expand All @@ -1652,7 +1655,7 @@ protected void parseOverlays(int series, long data, String suffix,
store.setLineFontSize(fontSize, i, 0);
}
store.setLineStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case SCALE_BAR:
Expand Down Expand Up @@ -1685,7 +1688,7 @@ protected void parseOverlays(int series, long data, String suffix,
store.setRectangleFontSize(fontSize, i, 0);
}
store.setRectangleStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case ELLIPSE:
Expand Down Expand Up @@ -1745,7 +1748,7 @@ else if (knots == 3) {
store.setEllipseFontSize(fontSize, i, 0);
}
store.setEllipseStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case CIRCLE:
Expand All @@ -1768,7 +1771,7 @@ else if (knots == 3) {
store.setEllipseFontSize(fontSize, i, 0);
}
store.setEllipseStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case CIRCLE_3POINT:
Expand Down Expand Up @@ -1808,7 +1811,7 @@ else if (knots == 3) {
store.setEllipseFontSize(fontSize, i, 0);
}
store.setEllipseStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case ANGLE:
Expand All @@ -1835,7 +1838,7 @@ else if (knots == 3) {
store.setPolylineFontSize(fontSize, i, 0);
}
store.setPolylineStrokeWidth(line, i, 0);
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case CLOSED_POLYLINE:
Expand Down Expand Up @@ -1875,7 +1878,7 @@ else if (knots == 3) {
store.setPolygonStrokeWidth(line, i, 0);
store.setPolygonID(shapeID, i, 0);
}
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
case CLOSED_BEZIER:
Expand Down Expand Up @@ -1915,7 +1918,7 @@ else if (knots == 3) {
}
store.setPolygonStrokeWidth(line, i, 0);
}
store.setImageROIRef(roiID, series, i);
store.setImageROIRef(roiID, series, roiRefIndex);

break;
default:
Expand Down