diff --git a/src/containers/MainPlotContainer/selectors.ts b/src/containers/MainPlotContainer/selectors.ts
index 00098c04..97304a4c 100644
--- a/src/containers/MainPlotContainer/selectors.ts
+++ b/src/containers/MainPlotContainer/selectors.ts
@@ -13,7 +13,11 @@ import {
     SELECTIONS_PLOT_NAME,
     THUMBNAIL_PATH,
 } from "../../constants";
-import { getCategoricalFeatureKeys, getMeasuredFeaturesDefs } from "../../state/metadata/selectors";
+import {
+    getCategoricalFeatureKeys,
+    getMeasuredFeaturesDefs,
+    getPerCellDataForPlot,
+} from "../../state/metadata/selectors";
 import {
     DataForPlot,
     FileInfo,
@@ -46,6 +50,7 @@ import {
     getLineMovingAverageWindow,
     getConnectByFeature,
     getConnectByCategory,
+    getFiltersToExclude,
 } from "../../state/selection/selectors";
 import {
     ColorForPlot,
@@ -288,15 +293,25 @@ export function calculateLinePlotData(
 }
 
 const getAnnotationData = createSelector(
-    [getFilteredCellData, getClickedCellsFileInfo, getPlotByOnX, getPlotByOnY, getHoveredCardId],
+    [
+        getPerCellDataForPlot,
+        getClickedCellsFileInfo,
+        getFiltersToExclude,
+        getPlotByOnX,
+        getPlotByOnY,
+        getGroupingCategoryNamesAsArray,
+        getHoveredCardId,
+    ],
     (
-        filteredCellData: DataForPlot,
+        allCellData: DataForPlot,
         clickedCellsFileInfo: FileInfo[],
+        filtersToExclude: string[],
         xAxis,
         yAxis,
+        groupByCategoryNames,
         currentHoveredCellId
     ): AnnotationData[] => {
-        if (isEmpty(filteredCellData.values) || isEmpty(filteredCellData.labels)) {
+        if (isEmpty(allCellData.values) || isEmpty(allCellData.labels)) {
             return [];
         }
         const initAcc: AnnotationData[] = [];
@@ -305,15 +320,23 @@ const getAnnotationData = createSelector(
             const fovID = data[FOV_ID_KEY] || "";
             const thumbnailPath = data[THUMBNAIL_PATH] || "";
 
-            const cellIds = filteredCellData.labels[ARRAY_OF_CELL_IDS_KEY];
-            // FileInfo is typed with `index` as optional because it gets added to the
-            // data from the database. However, at this point, index will always be defined, but since
-            // typescript doesn't know that, we still have this backup to find it in the
-            // id array but that code should never be executed.
+            const cellIds = allCellData.labels[ARRAY_OF_CELL_IDS_KEY];
+            // `FileInfo.index` is typed as optional because it is added from
+            // the database, but it will always be defined here. Note that
+            // `index` is the position in the full array of cell IDs, and does
+            // not account for filtering, so filtering needs to be done
+            // manually.
             const pointIndex =
                 data.index !== undefined ? data.index : findIndex(cellIds, (id) => id === cellID);
-            const x = filteredCellData.values[xAxis][pointIndex];
-            const y = filteredCellData.values[yAxis][pointIndex];
+            const x = allCellData.values[xAxis][pointIndex] ?? null;
+            const y = allCellData.values[yAxis][pointIndex] ?? null;
+
+            // Apply filtering
+            const groupName = groupByCategoryNames[pointIndex] ?? null;
+            if (filtersToExclude.includes(groupName)) {
+                return acc;
+            }
+
             if (pointIndex >= 0 && x !== null && y !== null) {
                 acc.push({
                     cellID,
diff --git a/src/containers/MainPlotContainer/test/selectors.test.ts b/src/containers/MainPlotContainer/test/selectors.test.ts
index 6f9d4aed..7dcf2299 100644
--- a/src/containers/MainPlotContainer/test/selectors.test.ts
+++ b/src/containers/MainPlotContainer/test/selectors.test.ts
@@ -51,8 +51,7 @@ describe("MainPlotContainer selectors", () => {
             const result: PlotlyAnnotation[] = getAnnotations(state);
             expect(result).to.have.lengthOf(2);
         });
-    });
-    describe("getAnnotations selector", () => {
+
         it("it filters out non visible points", () => {
             const state: State = {
                 ...newMockState,
@@ -66,8 +65,26 @@ describe("MainPlotContainer selectors", () => {
             const result: PlotlyAnnotation[] = getAnnotations(state);
             expect(result).to.have.lengthOf(0);
         });
-    });
-    describe("getAnnotations selector", () => {
+
+        it("it excludes filtered groups from annotations", () => {
+            const state: State = {
+                ...newMockState,
+                selection: {
+                    ...newMockState.selection,
+                    plotByOnX: "apical-proximity",
+                    plotByOnY: "apical-proximity",
+                    // 2 cells are selected, but the first (cell ID 1) will be
+                    // excluded by filtering
+                    selectedPoints: selectedCellFileInfo,
+                    filterExclude: ["Paxillin"],
+                },
+            };
+            const result: PlotlyAnnotation[] = getAnnotations(state);
+            expect(result).to.have.lengthOf(1);
+            expect(result[0].pointIndex).to.equal(1);
+            expect(result[0].cellID).to.equal("2");
+        });
+
         it("it still shows points whose values are zero", () => {
             const state: State = {
                 ...newMockState,
@@ -82,6 +99,7 @@ describe("MainPlotContainer selectors", () => {
             expect(result).to.have.lengthOf(2);
         });
     });
+
     describe("getXDisplayName", () => {
         it("returns the displayName for a continuous feature", () => {
             const state: State = {