aignostics 0.2.13__tar.gz → 0.2.16__tar.gz

{aignostics-0.2.13 → aignostics-0.2.16}/.gitignore

@@ -95,4 +95,4 @@ dist_vercel
 setup.sh.secret
 __marimo__
 notes.md
-CLAUDE.md
+CLAUDE.md

{aignostics-0.2.13 → aignostics-0.2.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.13
+Version: 0.2.16
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/

{aignostics-0.2.13 → aignostics-0.2.16}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.13",
+#     "aignostics==0.2.16",
 # ]
 # ///
 

{aignostics-0.2.13 → aignostics-0.2.16}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.13"
+version = "0.2.16"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -344,6 +344,7 @@ omit = [
     "*/_notebook.py",
     "*/_pydicom_handler.py",
     "*/_openslide_handler.py",
+    "*/qupath/*",
 ]
 branch = true
 parallel = true
@@ -354,7 +355,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.13"
+current_version = "0.2.16"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.13 → aignostics-0.2.16}/src/aignostics/application/_cli.py

@@ -376,7 +376,7 @@ def run_upload(
 
     total_bytes = 0
     for i, entry in enumerate(metadata_dict):
-        source = entry["source"]
+        source = entry["reference"]
         source_file_path = Path(source)
         if not source_file_path.is_file():
             logger.warning("Source file '%s' (row %d) does not exist", source_file_path, i)
@@ -403,8 +403,7 @@ def run_upload(
         def update_progress(bytes_uploaded: int, source: Path, platform_bucket_url: str) -> None:
             progress.update(task, advance=bytes_uploaded, description=f"{source.name}")
             for entry in metadata_dict:
-                if entry["source"] == str(source):
-                    entry["file_upload_progress"] = float(entry["file_upload_progress"]) + bytes_uploaded
+                if entry["reference"] == str(source):
                     entry["platform_bucket_url"] = platform_bucket_url
                     break
             write_metadata_dict_to_csv(

{aignostics-0.2.13 → aignostics-0.2.16}/src/aignostics/application/_gui.py

@@ -32,6 +32,9 @@ class PageBuilder(BasePageBuilder):
         from nicegui import app, background_tasks, binding, context, ui  # noq  # noqa: PLC0415
         from nicegui import run as nicegui_run  # noqa: PLC0415
 
+        if find_spec("paquo"):
+            from aignostics.qupath import Service as QuPathService  # noqa: PLC0415
+
         @binding.bindable_dataclass
         class SubmitForm:
             """Submit form."""
@@ -392,7 +395,10 @@ class PageBuilder(BasePageBuilder):
                             f"Selected folder {submit_form.source} to analyze."
                         ) if submit_form.wsi_step_label else None
                         submit_form.wsi_next_button.enable() if submit_form.wsi_next_button else None
-                        ui.notify(f"You chose directory {submit_form.source}.", type="info")
+                        ui.notify(
+                            f"You chose directory {submit_form.source}. Feel free to continue to the next step.",
+                            type="positive",
+                        )
                 else:
                     submit_form.source = None
                     submit_form.wsi_step_label.set_text(
@@ -413,7 +419,10 @@ class PageBuilder(BasePageBuilder):
                     f"Selected folder {submit_form.source} to analyze."
                 ) if submit_form.wsi_step_label else None
                 submit_form.wsi_next_button.enable() if submit_form.wsi_next_button else None
-                ui.notify(f"You chose directory {submit_form.source}.", type="info")
+                ui.notify(
+                    f"You chose directory {submit_form.source}. Feel free to continue to the next step.",
+                    type="positive",
+                )
 
             async def _on_wsi_next_click() -> None:
                 """Handle the 'Next' button click in WSI step.
@@ -443,6 +452,7 @@ class PageBuilder(BasePageBuilder):
                             Service.generate_metadata_from_source_directory,
                             str(submit_form.application_version_id),
                             submit_form.source,
+                            True,
                             [".*:staining_method=H&E"],
                         )
                         if submit_form.metadata_grid.options["rowData"] is None:
@@ -453,7 +463,8 @@ class PageBuilder(BasePageBuilder):
                         submit_form.wsi_spinner.set_visibility(False)
                         submit_form.metadata_grid.update()
                         ui.notify(
-                            f"Found {len(submit_form.metadata_grid.options['rowData'])} slides for analysis.",
+                            f"Found {len(submit_form.metadata_grid.options['rowData'])} slides for analysis."
+                            "Please provide missing metadata.",
                             type="positive",
                         )
                         stepper.next()
@@ -506,10 +517,13 @@ class PageBuilder(BasePageBuilder):
                     ui.button("Close", on_click=info_dialog.close)
 
             with ui.stepper().props("vertical").classes("w-full") as stepper:  # noqa: PLR1702
-                with ui.step("Application Version"):
+                with ui.step("Select Application Version"):
                     with ui.row().classes("w-full justify-center"):
                         with ui.column():
-                            ui.label(f"Select the version of {application.name} you want to run.")
+                            ui.label(
+                                f"Select the version of {application.name} you want to run. Not sure? "
+                                "Click “Next” to auto-select the latest version"
+                            )
                             ui.select(
                                 {version.application_version_id: version.version for version in application_versions},
                                 value=latest_application_version_id,
@@ -522,9 +536,9 @@ class PageBuilder(BasePageBuilder):
                             "BUTTON_APPLICATION_VERSION_NEXT"
                         )
 
-                with ui.step("Whole Slide Images"):
+                with ui.step("Select Whole Slide Images"):
                     submit_form.wsi_step_label = ui.label(
-                        "Select a folder with whole slide images you want to analyze."
+                        "Select the folder with the whole slide images you want to analyze then click Next."
                     )
                     with ui.stepper_navigation():
                         if "pytest" in sys.modules:
@@ -536,13 +550,21 @@ class PageBuilder(BasePageBuilder):
                         submit_form.wsi_spinner.set_visibility(False)
                         ui.button("Back", on_click=stepper.previous).props("flat")
 
-                with ui.step("Metadata"):
+                with ui.step("Choose Images and Edit Metadata"):
                     ui.markdown(
                         """
-                        1. Check extracted and provide missing metadata.
-                            Double click red cells to edit - you are done when all turned green.
-                        2. You can exclude slides from the analysis by selecting them and clicking "Exclude slides".
-                        3. You can revert to the original list by clicking the Back button.
+                        The Launchpad has found all compatible slide files in your selected folder.
+
+                        1. Check the slides that have been found.
+                            If you wish to exclude any from analysis at this point, check the boxes next to those slides
+                            and click “Exclude” to remove them.
+                        2. For the slides you wish to analyze,
+                            provide the missing metadata to finalize the upload.
+                            Double click red cells to edit the missing data with the available options.
+                        3. Once all the metadata has been added and your slide selection has been finalized,
+                            click “Next”.
+
+                        You can revert to the previous step and reupload at any point by clicking “Back”.
                         """
                     )
 
@@ -616,7 +638,8 @@ class PageBuilder(BasePageBuilder):
                             submit_form.metadata = await submit_form.metadata_grid.get_client_data()
                         _upload_ui.refresh(submit_form.metadata)
                         submit_form.submission_upload_button.enable()
-                        ui.notify("Prepared upload UI.", type="info")
+                        if "pytest" in sys.modules:
+                            ui.notify("Prepared upload UI.", type="info")
                         stepper.next()
 
                     async def _delete_selected() -> None:
@@ -662,7 +685,7 @@ class PageBuilder(BasePageBuilder):
                     submit_form.metadata_grid = (
                         ui.aggrid({
                             "columnDefs": [
-                                {"headerName": "Reference", "field": "reference", "checkboxSelection": True},
+                                {"headerName": "Reference", "field": "reference_short", "checkboxSelection": True},
                                 {
                                     "headerName": "Thumbnail",
                                     "field": "thumbnail",
@@ -750,7 +773,6 @@ class PageBuilder(BasePageBuilder):
                         .on("selectionChanged", _handle_grid_selection_changed)
                         .mark("GRID_METADATA")
                     )
-                    # .style("height: auto; width: 1000px")
                     # use ui timer to update the grid class depending on dark mode, with a frequency of once per second
                     ui.timer(
                         interval=1,
@@ -768,15 +790,33 @@ class PageBuilder(BasePageBuilder):
                     with ui.stepper_navigation():
                         if "pytest" in sys.modules:
                             ui.button("Select", on_click=_pytest_meta, icon="folder").mark("BUTTON_PYTEST_META")
+                        submit_form.metadata_next_button = ui.button("Next", on_click=_metadata_next)
+                        submit_form.metadata_next_button.mark("BUTTON_METADATA_NEXT").disable()
                         submit_form.metadata_exclude_button = ui.button(
                             "Exclude selected", on_click=_delete_selected
                         ).mark("BUTTON_DELETE_SELECTED")
                         submit_form.metadata_exclude_button.set_text("Exclude")
                         submit_form.metadata_exclude_button.disable()
-                        submit_form.metadata_next_button = ui.button("Next", on_click=_metadata_next)
-                        submit_form.metadata_next_button.mark("BUTTON_METADATA_NEXT").disable()
                         ui.button("Back", on_click=stepper.previous).props("flat")
 
+                def _submit() -> None:
+                    """Submit the application run."""
+                    ui.notify("Submitting application run ...", type="info")
+                    try:
+                        run = service.application_run_submit_from_metadata(
+                            str(submit_form.application_version_id),
+                            submit_form.metadata or [],
+                        )
+                    except Exception as e:  # noqa: BLE001
+                        ui.notify(f"Failed to submit application run: {e}.", type="warning")
+                        return
+                    ui.notify(
+                        f"Application run submitted with id '{run.application_run_id}'. "
+                        "Navigating to application run ...",
+                        type="positive",
+                    )
+                    ui.navigate.to(f"/application/run/{run.application_run_id}")
+
                 async def _upload() -> None:
                     """Upload prepared slides."""
                     if submit_form.submission_submit_button is None or submit_form.submission_upload_button is None:
@@ -796,12 +836,13 @@ class PageBuilder(BasePageBuilder):
                     ui.notify("Upload to Aignostics Platform completed.", type="positive")
                     submit_form.submission_submit_button.enable()
                     submit_form.submission_upload_button.disable()
+                    _submit()
 
                 @ui.refreshable
                 def _upload_ui(metadata: list[dict[str, Any]]) -> None:
                     """Upload UI."""
                     with ui.column(align_items="start"):
-                        ui.label(f"1. Upload {len(metadata)} slides you prepared to the Aignostics Platform.")
+                        ui.label(f"Upload and submit your {len(metadata)} slide(s) for analysis.")
                         upload_complete = True
                         for row in metadata or []:
                             upload_complete = upload_complete and row["file_upload_progress"] == 1
@@ -809,11 +850,6 @@ class PageBuilder(BasePageBuilder):
                                 with ui.circular_progress(value=row["file_upload_progress"], show_value=False):
                                     ui.button(icon="cloud_upload").props("flat round").disable()
                                 ui.label(f"{row['source']} ({row['file_size_human']})").classes("w-4/5")
-                        if upload_complete:
-                            ui.label(
-                                f"2. All uploads completed successfully. Click submit to run "
-                                f"{submit_form.application_version_id} on {len(metadata)} slides."
-                            )
 
                 def _update_upload_progress() -> None:
                     """Update the upload progress for each file."""
@@ -832,28 +868,14 @@ class PageBuilder(BasePageBuilder):
                                         break
                         _upload_ui.refresh(submit_form.metadata)
 
-                def _submit() -> None:
-                    """Submit the application run."""
-                    ui.notify("Submitting application run ...", type="info")
-                    try:
-                        run = service.application_run_submit_from_metadata(
-                            str(submit_form.application_version_id),
-                            submit_form.metadata or [],
-                        )
-                    except Exception as e:  # noqa: BLE001
-                        ui.notify(f"Failed to submit application run: {e}.", type="warning")
-                        return
-                    ui.notify(f"Application run submitted with id '{run.application_run_id}'.", type="positive")
-                    ui.navigate.to(f"/application/run/{run.application_run_id}")
-
-                with ui.step("Submission"):
+                with ui.step("Slide Submission"):
                     _upload_ui([])
                     upload_message_queue = Manager().Queue()
                     ui.timer(0.1, callback=_update_upload_progress)
 
                     with ui.stepper_navigation():
                         submit_form.submission_upload_button = ui.button(
-                            "Upload",
+                            "Upload and Submit",
                             on_click=_upload,
                             icon="check",
                         ).mark("BUTTON_SUBMISSION_UPLOAD")
@@ -862,6 +884,7 @@ class PageBuilder(BasePageBuilder):
                             on_click=_submit,
                             icon="check",
                         )
+                        submit_form.submission_submit_button.set_visibility(False)
                         submit_form.submission_submit_button.mark("BUTTON_SUBMISSION_SUBMIT").disable()
                         ui.button("Back", on_click=stepper.previous).props("flat")
 
@@ -906,8 +929,8 @@ class PageBuilder(BasePageBuilder):
                 ui.notify(f"Canceling application run with id '{run_id}' ...", type="info")
                 try:
                     service.application_run_cancel(run_id)
-                    ui.notify("Application run cancelled!", type="positive")
                     ui.navigate.reload()
+                    ui.notify("Application run cancelled!", type="positive")
                     return True
                 except Exception as e:  # noqa: BLE001
                     ui.notify(f"Failed to cancel application run: {e}.", type="warning")
@@ -934,11 +957,14 @@ class PageBuilder(BasePageBuilder):
                         selected_folder.value = str(Path.home())
 
                     ui.label("Select a folder to download all results for this application run.")
-                    ui.button("Use Home", on_click=_select_home, icon="home").mark("BUTTON_DOWNLOAD_DESTINATION_HOME")
-                    ui.space()
-                    ui.button("Select Download Folder", on_click=_select_download_destination, icon="folder_open").mark(
-                        "BUTTON_DOWNLOAD_DESTINATION_SELECT"
-                    )
+                    with ui.row().classes("w-full"):
+                        ui.button("Use Home", on_click=_select_home, icon="home").mark(
+                            "BUTTON_DOWNLOAD_DESTINATION_HOME"
+                        )
+                        ui.space()
+                        ui.button(
+                            "Select Download Folder", on_click=_select_download_destination, icon="folder_open"
+                        ).mark("BUTTON_DOWNLOAD_DESTINATION_SELECT")
 
                 download_item_status = ui.label("")
                 download_item_status.set_visibility(False)
@@ -1004,7 +1030,7 @@ class PageBuilder(BasePageBuilder):
                     ui.notify("Download completed.", type="positive")
 
                 ui.separator()
-                with ui.row(align_items="end").classes("w-full"):
+                with ui.row(align_items="end").classes("w-full justify-end"):
                     ui.button("Close", on_click=download_run_dialog.close, color="secondary").props("outline").mark(
                         "DIALOG_BUTTON_DOWNLOAD_CLOSE"
                     )
@@ -1013,7 +1039,7 @@ class PageBuilder(BasePageBuilder):
                         "DIALOG_BUTTON_DOWNLOAD_RUN"
                     )
 
-            with ui.dialog() as qupath_project_create_dialog, ui.card().style(WIDTH_1200px):
+            with ui.dialog() as qupath_project_create_dialog, ui.card().style(WIDTH_1200px):  # noqa: F841
                 ui.button("Select QuPath folder")
                 with ui.row(align_items="end").classes("w-full"), ui.column(align_items="end").classes("w-full"):
                     ui.button("Close", on_click=download_run_dialog.close)
@@ -1078,11 +1104,14 @@ class PageBuilder(BasePageBuilder):
 
             if run_data and run_data.status.value == ApplicationRunStatus.COMPLETED:
                 with ui.row().classes("w-full justify-end"):
-                    if find_spec("paquo"):
+                    if find_spec("paquo") and QuPathService.find_qupath():
                         ui.button(
                             "Open in QuPath Microscopy Viewer",
                             icon="zoom_in",
-                            on_click=qupath_project_create_dialog.open,
+                            on_click=lambda: (
+                                ui.notify("Opening QuPath ...", type="info"),  # type: ignore[func-returns-value]
+                                QuPathService.launch_qupath(),
+                            ),
                         )
                     if find_spec("marimo"):
                         ui.button(

{aignostics-0.2.13 → aignostics-0.2.16}/src/aignostics/application/_service.py

@@ -311,12 +311,13 @@ class Service(BaseService):
     def generate_metadata_from_source_directory(
         application_version_id: str,
         source_directory: Path,
+        with_gui_metadata: bool = False,
         mappings: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """Generate metadata from the source directory.
 
         Steps:
-        1. Recursively files ending with .tiff, .tif and .dcm in the source directory
+        1. Recursively files ending with .tiff, .tif, .svs and .dcm in the source directory
         2. Creates a dict with the following columns
             - reference (str): The reference of the file, by default equivalent to the absolute file name
             - source (str): The absolute filename
@@ -331,6 +332,7 @@ class Service(BaseService):
             application_version_id (str): The ID of the application version.
                 If application id is given, the latest version of that application is used.
             source_directory (Path): The source directory to generate metadata from.
+            with_gui_metadata (bool): If True, include additional metadata for GUI.
             mappings (list[str]): Mappings of the form '<regexp>:<key>:<value>,<key>:<value>,...'.
                 The regular expression is matched against the reference attribute of the entry.
                 The key/value pairs are applied to the entry if the pattern matches.
@@ -350,7 +352,7 @@ class Service(BaseService):
         application_version = Service().application_version(application_version_id, use_latest_if_no_version_given=True)  # noqa: F841
 
         metadata = []
-        file_extensions = [".tiff", ".tif", ".dcm"]
+        file_extensions = [".tiff", ".tif", ".svs", ".dcm"]
 
         try:
             for extension in file_extensions:
@@ -361,31 +363,42 @@ class Service(BaseService):
                         while chunk := f.read(1024):
                             hash_sum.update(chunk)  # type: ignore[no-untyped-call]
                     checksum = str(base64.b64encode(hash_sum.digest()), "UTF-8")  # type: ignore[no-untyped-call]
-                    image_metadata = WSIService().get_metadata(file_path)
-                    width = image_metadata["dimensions"]["width"]
-                    height = image_metadata["dimensions"]["height"]
-                    mpp = image_metadata["resolution"]["mpp_x"]
-                    file_size_human = image_metadata["file"]["size_human"]
-                    reference = file_path.absolute()
-                    entry = {
-                        "reference": str(reference),
-                        "source": str(file_path),
-                        "checksum_base64_crc32c": checksum,
-                        "resolution_mpp": mpp,
-                        "width_px": width,
-                        "height_px": height,
-                        "staining_method": None,
-                        "tissue": None,
-                        "disease": None,
-                        "file_size_human": file_size_human,
-                        "file_upload_progress": 0.0,
-                        "platform_bucket_url": None,
-                    }
-
-                    if mappings:
-                        Service._apply_mappings_to_entry(entry, mappings)
-
-                    metadata.append(entry)
+                    try:
+                        image_metadata = WSIService().get_metadata(file_path)
+                        width = image_metadata["dimensions"]["width"]
+                        height = image_metadata["dimensions"]["height"]
+                        mpp = image_metadata["resolution"]["mpp_x"]
+                        file_size_human = image_metadata["file"]["size_human"]
+                        reference = file_path.absolute()
+                        entry = {
+                            "reference": str(reference),
+                            "reference_short": str(reference.name),
+                            "source": str(file_path),
+                            "checksum_base64_crc32c": checksum,
+                            "resolution_mpp": mpp,
+                            "width_px": width,
+                            "height_px": height,
+                            "staining_method": None,
+                            "tissue": None,
+                            "disease": None,
+                            "file_size_human": file_size_human,
+                            "file_upload_progress": 0.0,
+                            "platform_bucket_url": None,
+                        }
+                        if not with_gui_metadata:
+                            entry.pop("reference_short", None)
+                            entry.pop("source", None)
+                            entry.pop("file_size_human", None)
+                            entry.pop("file_upload_progress", None)
+
+                        if mappings:
+                            Service._apply_mappings_to_entry(entry, mappings)
+
+                        metadata.append(entry)
+                    except Exception:
+                        message = f"Failed to process file '{file_path}'"
+                        logger.exception(message)
+                        continue
 
             logger.debug("Generated metadata for %d files", len(metadata))
             return metadata
@@ -421,9 +434,9 @@ class Service(BaseService):
         application_version = Service().application_version(application_version_id, use_latest_if_no_version_given=True)
         for row in metadata:
             reference = row["reference"]
-            source_file_path = Path(row["source"])
+            source_file_path = Path(row["reference"])
             if not source_file_path.is_file():
-                logger.warning("Source file '%s' does not exist.", row["source"])
+                logger.warning("Source file '%s' does not exist.", row["referebce"])
                 return False
             object_key = (
                 f"{psutil.Process().username()}/{upload_prefix}/"
@@ -583,9 +596,9 @@ class Service(BaseService):
                                 "width_px": int(row["width_px"]),
                                 "media_type": (
                                     "image/tiff"
-                                    if row["source"].lower().endswith((".tif", ".tiff"))
+                                    if row["reference"].lower().endswith((".tif", ".tiff"))
                                     else "application/dicom"
-                                    if row["source"].lower().endswith(".dcm")
+                                    if row["reference"].lower().endswith(".dcm")
                                     else "application/octet-stream"
                                 ),
                                 "resolution_mpp": float(row["resolution_mpp"]),

{aignostics-0.2.13 → aignostics-0.2.16}/src/aignostics/dataset/_gui.py

@@ -42,21 +42,46 @@ class PageBuilder(BasePageBuilder):
                 # No need to do anything here
                 pass
             with ui.row(align_items="start").classes("full-width"):
-                ui.markdown("""
-                    ##### Download DICOM datasets from IDC Portal of NCI
-                    1. Click 🔍 Explore Portal to find DICOM datasets of interest.
-                    2. Find a collection, patient case, study, series, or instance of interest,
-                        and copy one or multiple IDs into the field below.
-                    3. If you don't want to explore, simply click on "Example Dataset".
-                    4. Use ⌂ Home or 📁 select a download folder and hit ↓ download.
-                    5. Run Applications via the ☰ menu, select an application, and the folder
-                    """).classes("w-3/5")
+                ui.markdown(
+                    """
+                    ### Download public DICOM datasets
+                    Explore the IDC Portal from NCI to find datasets of interest and upload them to the Launchpad
+                    to test Aignostics applications.
+                    """
+                ).classes("w-3/5")
                 ui.space()
                 with ui.column().classes("w-1/5"):
                     ui.image("/assets/NIH-IDC-logo.svg").classes("w-25").style("margin-top:1.25rem")
                     with ui.link(target=PORTAL_URL, new_tab=True):
                         ui.button("Explore Portal", icon="search")
 
+            with ui.row(align_items="start").classes("w-full"):
+                ui.markdown("""
+                    ##### Pick a Dataset
+                    1. Click “Explore Portal” on the right and find a DICOM dataset of interest
+                    2. Copy the UID into the field below
+                    """).classes("w-2/5")
+                ui.space()
+                ui.label("OR").style("margin-top: 2rem; font-size: 2rem; color: grey")
+                ui.space()
+                ui.markdown("""
+                    ##### Quick Start
+                    1. Click “Use Example Dataset” below to automatically populate a pre-selected DICOM dataset
+                    """).classes("w-2/5")
+
+            with ui.row(align_items="start").classes("w-full"):
+                ui.markdown(
+                    """
+                    Once your dataset UID is added, click "Use Home" or “Select Download Folder” and select a
+                    folder on your computer for the dataset to be stored.
+                    Once you've chosen, the “Download” button should light up and you can download your
+                    selected dataset.
+
+                    When you're ready to begin image analysis, open ☰ menu and click “Run Applications” to return to
+                    the main menu.
+                    """
+                )
+
             def _on_source_input_change(e: ValueChangeEventArguments) -> None:
                 """On change event."""
                 if download_form.download_button is None:
@@ -192,6 +217,11 @@ class PageBuilder(BasePageBuilder):
                         color="secondary",
                     ).mark("BUTTON_EXAMPLE_DATASET")
                     ui.space()
+                    ui.button("Use Home", on_click=_select_home, icon="home").mark("BUTTON_DOWNLOAD_DESTINATION_HOME")
+                    ui.button("Select Download Folder", on_click=_select_destination, icon="folder").mark(
+                        "BUTTON_DOWNLOAD_DESTINATION"
+                    )
+                    ui.space()
                     with ui.row(align_items="center"):
                         download_form.download_button = ui.button("Download", icon="cloud_download").mark(
                             "BUTTON_DOWNLOAD"
@@ -204,11 +234,6 @@ class PageBuilder(BasePageBuilder):
                         with download_form.download_progress:
                             ui.button(icon="cloud_download").props("flat round").disable()
                         download_form.download_progress.visible = False
-                    ui.space()
-                    ui.button("Use Home", on_click=_select_home, icon="home").mark("BUTTON_DOWNLOAD_DESTINATION_HOME")
-                    ui.button("Select Download Folder", on_click=_select_destination, icon="folder").mark(
-                        "BUTTON_DOWNLOAD_DESTINATION"
-                    )
 
             download_message_queue = Manager().Queue()