diff --git a/client/src/components/Panels/Common/ToolSection.vue b/client/src/components/Panels/Common/ToolSection.vue
index 66e7d912cff5..1e3a668944ee 100644
--- a/client/src/components/Panels/Common/ToolSection.vue
+++ b/client/src/components/Panels/Common/ToolSection.vue
@@ -3,7 +3,7 @@ import { computed, onMounted, onUnmounted, ref, watch } from "vue";
 
 import { eventHub } from "@/components/plugins/eventHub.js";
 import { useConfig } from "@/composables/config";
-import { type Tool as ToolType } from "@/stores/toolStore";
+import { type Tool as ToolType, type ToolSectionLabel as LabelType } from "@/stores/toolStore";
 import { useToolStore } from "@/stores/toolStore";
 import { type Workflow } from "@/stores/workflowStore";
 import ariaAlert from "@/utils/ariaAlert";
@@ -66,7 +66,15 @@ const elems = computed(() => {
         return props.category.elems;
     }
     if (props.category.tools !== undefined && props.category.tools.length > 0) {
-        return props.category.tools.map((toolId: string) => toolStore.getToolForId(toolId));
+        return props.category.tools.map((toolId: string) => {
+            const tool = toolStore.getToolForId(toolId);
+            if (!tool && toolId.startsWith("panel_label_") && props.category.panel_labels) {
+                const labelId = toolId.split("panel_label_")[1];
+                return props.category.panel_labels.find((label: LabelType) => label.id === labelId);
+            } else {
+                return tool;
+            }
+        });
     }
     return [];
 });
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index 21352e49483f..1680c29fc3da 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -9,7 +9,7 @@ import { useRouter } from "vue-router/composables";
 import { getGalaxyInstance } from "@/app";
 import { useGlobalUploadModal } from "@/composables/globalUploadModal";
 import { getAppRoot } from "@/onload/loadConfig";
-import { type Tool, type ToolSection as ToolSectionType } from "@/stores/toolStore";
+import { type Tool, type ToolSection as ToolSectionType, type ToolSectionLabel } from "@/stores/toolStore";
 import { useToolStore } from "@/stores/toolStore";
 import { Workflow, type Workflow as WorkflowType } from "@/stores/workflowStore";
 import localize from "@/utils/localization";
@@ -92,14 +92,24 @@ const dataManagerSection = computed(() => {
 
 /** `toolsById` from `toolStore`, except it only has valid tools for `props.workflow` value */
 const localToolsById = computed(() => {
-    // Filter the items with is_compat === true
+    const addedToolTexts: string[] = [];
     if (toolStore.toolsById && Object.keys(toolStore.toolsById).length > 0) {
-        const toolEntries = Object.entries(toolStore.toolsById).filter(
-            ([_, tool]: [string, any]) =>
+        const toolEntries = Object.entries(toolStore.toolsById).filter(([_, tool]: [string, any]) => {
+            // filter out duplicate tools (different ids, same exact name+description)
+            // related ticket: https://github.com/galaxyproject/galaxy/issues/16145
+            const toolText: string = tool.name + tool.description;
+            if (addedToolTexts.includes(toolText)) {
+                return false;
+            } else {
+                addedToolTexts.push(toolText);
+            }
+            // filter on non-hidden, non-disabled, and workflow compatibile (based on props.workflow)
+            return (
                 !tool.hidden &&
                 tool.disabled !== true &&
                 (props.workflow ? tool.is_workflow_compatible : !SECTION_IDS_TO_EXCLUDE.includes(tool.panel_section_id))
-        );
+            );
+        });
         return Object.fromEntries(toolEntries);
     }
     return {};
@@ -111,7 +121,15 @@ const localSectionsById = computed(() => {
     // for all values that are `ToolSection`s, filter out tools that aren't in `localToolsById`
     const sectionEntries = Object.entries(currentPanel.value).map(([id, section]: [string, any]) => {
         if (section.tools && Array.isArray(section.tools)) {
-            section.tools = section.tools.filter((tool: string) => validToolIdsInCurrentView.includes(tool));
+            section.tools = section.tools.filter((toolId: string) => {
+                if (validToolIdsInCurrentView.includes(toolId)) {
+                    return true;
+                } else if (toolId.startsWith("panel_label_") && section.panel_labels) {
+                    // panel_label_ is a special case where there is a label within a section
+                    const labelId = toolId.split("panel_label_")[1];
+                    return section.panel_labels.find((label: ToolSectionLabel) => label.id === labelId) !== undefined;
+                }
+            });
         }
         return [id, section];
     });
diff --git a/client/src/stores/toolStore.ts b/client/src/stores/toolStore.ts
index 43dac1f78be0..ae799f972569 100644
--- a/client/src/stores/toolStore.ts
+++ b/client/src/stores/toolStore.ts
@@ -36,7 +36,18 @@ export interface ToolSection {
     version?: string;
     description?: string;
     links?: Record<string, string>;
-    tools: string[];
+    tools?: string[];
+    elems?: ToolSection[];
+    panel_labels?: string[];
+}
+
+export interface ToolSectionLabel {
+    model_class: string;
+    id: string;
+    text: string;
+    version?: string;
+    description?: string | null;
+    links?: Record<string, string> | null;
 }
 
 // TODO: Use this in ToolSearch.vue
@@ -147,8 +158,8 @@ export const useToolStore = defineStore("toolStore", () => {
             await axios
                 .get(`${getAppRoot()}api/tools?in_panel=False`)
                 .then(({ data }) => {
-                    loading.value = false;
                     saveAllTools(data.tools);
+                    loading.value = false;
                 })
                 .catch((error) => {
                     console.error(error);
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index b28cbac33558..2a6b28aed697 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1326,7 +1326,7 @@ def to_panel_view(self, trans, in_panel=True, tool_help=False, view=None, **kwds
                 view = self._default_panel_view
             view_contents = {}
             rval[view] = view_contents
-            panel_elts = list(self.tool_panel_contents(trans, view=view, **kwds))
+            panel_elts = self.tool_panel_contents(trans, view=view, **kwds)
             for elt in panel_elts:
                 # Only use cache for objects that are Tools.
                 if hasattr(elt, "tool_type"):
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 8eb65a9d660c..5d49f0aea76f 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -74,10 +74,18 @@ def copy(self):
         return copy
 
     def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None, only_ids=False):
-        """Return a dict that includes section's attributes."""
+        """Return a dict that includes section's attributes.
+
+        if `only_ids` is `True`, we store only the ids of the section's tools in `section.tools`
+        (and full `ToolSectionLabel` objects in `section.panel_labels` if any are present)
+
+        if `only_ids` is `False`, we store the section's full `Tool` (and any other) objects in
+        `section.elems`
+        """
 
         section_dict = super().to_dict()
         section_elts = []
+        section_panel_labels = []
         kwargs = dict(trans=trans, link_details=link_details, tool_help=tool_help)
         for elt in self.elems.values():
             if hasattr(elt, "tool_type") and toolbox:
@@ -85,11 +93,18 @@ def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None, only
                     section_elts.append(elt.id)
                 else:
                     section_elts.append(toolbox.get_tool_to_dict(trans, elt, tool_help=tool_help))
-            elif only_ids is False:
-                section_elts.append(elt.to_dict(**kwargs))
+            else:
+                # if section has a ToolSectionLabel within it
+                if only_ids and elt.text:
+                    section_panel_labels.append(elt.to_dict(**kwargs))
+                    section_elts.append("panel_label_" + str(elt.id))
+                else:
+                    section_elts.append(elt.to_dict(**kwargs))
 
         if only_ids:
             section_dict["tools"] = section_elts
+            if section_panel_labels:
+                section_dict["panel_labels"] = section_panel_labels
         else:
             section_dict["elems"] = section_elts
 
@@ -98,6 +113,7 @@ def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None, only
     def panel_items(self):
         return self.elems
 
+
 class ToolSectionLabel(Dictifiable):
     """
     A label for a set of tools that can be displayed above groups of tools