diff --git a/annotating_with_checks.py b/annotating_with_checks.py
new file mode 100644
index 0000000..0ad8c77
--- /dev/null
+++ b/annotating_with_checks.py
@@ -0,0 +1,258 @@
+import sys
+import os
+import json
+import shutil
+import concurrent.futures
+import threading
+
+# Fix for Matplotlib in threads: Set backend to non-interactive 'Agg'
+import matplotlib
+matplotlib.use('Agg')
+
+from PIL import Image, ImageDraw, ImageFont
+import annotating
+from annotating import MARGIN_LEFT, ANNOT_WIDTH
+
+# Global lock for Matplotlib/Latex rendering to prevent race conditions
+LATEX_LOCK = threading.Lock()
+
+BOX_SIZE = 30
+SCORE_BOX_SIZE = 30
+SCORES = [x * 0.5 for x in range(9)]  # 0.0 to 4.0
+
+try:
+    CHECKBOX_FONT = ImageFont.truetype("DejaVuSans.ttf", 20)
+except IOError:
+    try:
+        CHECKBOX_FONT = ImageFont.truetype("arial.ttf", 20)
+    except IOError:
+        CHECKBOX_FONT = ImageFont.load_default()
+
+def draw_checkbox(draw, x, y, size=BOX_SIZE, label=None, fill="white"):
+    if label:
+        draw.text((x - BOX_SIZE-5, y + 2), str(label), fill="black", font=CHECKBOX_FONT)
+    draw.rectangle([x, y, x + size, y + size], fill=fill, outline="black", width=2)
+
+    return [x, y, x + size, y + size]
+
+def safe_render_latex(text, **kwargs):
+    """Thread-safe wrapper for latex rendering."""
+    with LATEX_LOCK:
+        return annotating.render_latex_text(text, **kwargs)
+
+def create_base_image(pdf_path):
+    """Converts PDF pages to a single vertically stacked image."""
+    try:
+        pages = annotating.convert_from_path(pdf_path)
+        total_h = sum(page.height for page in pages)
+        max_w = max(page.width for page in pages)
+        base_img = Image.new("RGBA", (max_w, total_h), "white")
+        cy = 0
+        for page in pages:
+            base_img.paste(page.convert("RGBA"), (0, cy))
+            cy += page.height
+        return base_img
+    except Exception:
+        return None
+
+def render_header(label, score, feedbacks, base_width):
+    """Generates the score line and global feedback elements."""
+    elements = []
+
+    # Score Line
+    score_text_img = safe_render_latex(f"{label} ; Note : {score}", width_px=base_width // 2, fontsize=18)
+    score_line_h = max(score_text_img.height, SCORE_BOX_SIZE + 10)
+    score_line_img = Image.new("RGBA", (base_width, score_line_h), (255, 255, 255, 0))
+    score_line_img.paste(score_text_img, (0, 0))
+
+    draw_score = ImageDraw.Draw(score_line_img)
+    start_x = score_text_img.width + 20
+    local_boxes = []
+
+    for val in SCORES:
+        box = draw_checkbox(draw_score, start_x, 5, SCORE_BOX_SIZE, str(val))
+        local_boxes.append({
+            "type": "score", "label": label, "value": val,
+            "rel_box": box, "elem_y": 0
+        })
+        start_x += SCORE_BOX_SIZE + 60
+    elements.append((score_line_img, local_boxes))
+
+    # Global Feedback
+    for i, fb in enumerate(feedbacks):
+        fb_img = safe_render_latex(fb['text'], width_px=base_width)
+        draw_fb = ImageDraw.Draw(fb_img)
+        bx = fb_img.width - BOX_SIZE - 5
+        by = 5
+        box = draw_checkbox(draw_fb, bx, by, BOX_SIZE)
+
+        elements.append((fb_img, [{
+            "type": "del_global", "label": label, "index": i,
+            "text_preview": fb['text'][:20], "rel_box": box, "elem_y": 0
+        }]))
+
+    return elements
+
+def process_label(root_dir, student_id, label, content):
+    """Processes a single label (PDF) -> Annotated Image + Checkboxes."""
+    copie_folder = f"Copie{student_id}"
+    pdf_path = os.path.join(root_dir, copie_folder, f"{label}.pdf")
+
+    if not os.path.exists(pdf_path):
+        return None, []
+
+    base_img = create_base_image(pdf_path)
+    if not base_img:
+        return None, []
+
+    # Extract Data
+    coordinates = content.get('coordinates', (0, 0))
+    hmin = coordinates[0]
+    result = content.get('result', {})
+    score = result.get('score', 0)
+    feedbacks = result.get('feedback', [])
+
+    global_fb = [f for f in feedbacks if not f.get('box_2d')]
+    local_fb = [f for f in feedbacks if f.get('box_2d')]
+    local_fb.sort(key=lambda x: x['box_2d'][0])
+
+    checkbox_map = []
+
+    # 1. Render Header
+    header_elements = render_header(label, score, global_fb, base_img.width)
+    header_height = sum(x[0].height for x in header_elements)
+
+    # 2. Assemble Base + Header
+    total_height = base_img.height + header_height
+    final_img = Image.new("RGB", (base_img.width + MARGIN_LEFT, total_height), "white")
+
+    current_y = 0
+    for img, boxes in header_elements:
+        final_img.paste(img, (0, current_y))
+        for b in boxes:
+            b['final_box'] = [b['rel_box'][0], b['rel_box'][1] + current_y,
+                              b['rel_box'][2], b['rel_box'][3] + current_y]
+            checkbox_map.append(b)
+        current_y += img.height
+
+    image_offset_y = current_y
+    final_img.paste(base_img, (MARGIN_LEFT, image_offset_y))
+
+    # 3. Draw Local Annotations
+    draw = ImageDraw.Draw(final_img, "RGBA")
+    last_text_bottom = 0
+
+    for i, fb in enumerate(local_fb):
+        box = fb.get('box_2d')
+        if not box: continue
+
+        ymin, xmin, ymax, xmax = box
+        target_ymin = (ymin - hmin) + image_offset_y
+        target_ymax = (ymax - hmin) + image_offset_y
+        target_xmin = xmin + MARGIN_LEFT
+        target_xmax = xmax + MARGIN_LEFT
+
+        draw.rectangle([target_xmin, target_ymin, target_xmax, target_ymax], outline="red", width=3)
+
+        rect_cb_box = draw_checkbox(draw, target_xmax - BOX_SIZE, target_ymin, BOX_SIZE)
+        checkbox_map.append({
+            "type": "del_local", "label": label, "index": i,
+            "text_preview": fb['text'][:20], "final_box": rect_cb_box
+        })
+
+        txt_img_raw = safe_render_latex(fb['text'], width_px=ANNOT_WIDTH, bg_color=(255, 200, 200, 180), max_lines=3)
+        container_h = max(txt_img_raw.height, BOX_SIZE)
+        txt_img = Image.new("RGBA", (ANNOT_WIDTH, container_h), (255, 255, 255, 0))
+        txt_img.paste(txt_img_raw, (0, 0))
+
+        d_txt = ImageDraw.Draw(txt_img)
+        draw_checkbox(d_txt, ANNOT_WIDTH - BOX_SIZE, 0, BOX_SIZE)
+
+        center_y = (target_ymin + target_ymax) / 2
+        paste_y = max(center_y - (txt_img.height / 2), image_offset_y)
+        if paste_y < last_text_bottom: paste_y = last_text_bottom + 5
+
+        req_h = int(paste_y + txt_img.height + 20)
+        if req_h > final_img.height:
+            new_final = Image.new("RGB", (final_img.width, req_h), "white")
+            new_final.paste(final_img, (0,0))
+            final_img = new_final
+            draw = ImageDraw.Draw(final_img, "RGBA")
+
+        final_img.paste(txt_img, (10, int(paste_y)), mask=txt_img)
+        checkbox_map.append({
+            "type": "del_local", "label": label, "index": i,
+            "text_preview": fb['text'][:20],
+            "final_box": [10 + ANNOT_WIDTH - BOX_SIZE, int(paste_y), 10 + ANNOT_WIDTH, int(paste_y) + BOX_SIZE]
+        })
+        last_text_bottom = paste_y + txt_img.height
+
+    return final_img, checkbox_map
+
+import re
+def natural_key(text):
+        return [int(c) if c.isdigit() else c.lower() for c in re.split(r'(\d+)', str(text))]
+
+def process_student(args):
+    """Thread worker: Processes one student."""
+    root_dir, student_id, labels = args
+    print(f"Generating Checkable PDF for: {student_id}")
+
+    output_dir = os.path.join(root_dir, "Bnot", f"Copie{student_id}")
+    if os.path.exists(output_dir):
+        shutil.rmtree(output_dir)
+    os.makedirs(output_dir)
+
+    label_images = []
+    student_checkboxes = []
+    processed_labels_order = []
+
+    for label, content in sorted(labels.items(), key=lambda x: natural_key(x[0])):
+        img, boxes = process_label(root_dir, student_id, label, content)
+        if img:
+            label_images.append(img)
+            student_checkboxes.append(boxes)
+            processed_labels_order.append(label)
+
+    if not label_images:
+        return
+
+    max_w = max(i.width for i in label_images)
+    total_h = sum(i.height for i in label_images)
+    concat_img = Image.new("RGB", (max_w, total_h), "white")
+
+    final_json_map = []
+    current_y = 0
+
+    for label_name, img, boxes in zip(processed_labels_order, label_images, student_checkboxes):
+        concat_img.paste(img, (0, current_y))
+
+        for item in boxes:
+            b = item['final_box']
+            item['global_box'] = [b[0], b[1] + current_y, b[2], b[3] + current_y]
+            final_json_map.append(item)
+
+        current_y += img.height
+
+    with open(os.path.join(output_dir, "checkboxes.json"), "w") as f:
+        json.dump(final_json_map, f, indent=2)
+
+    concat_img.save(os.path.join(output_dir, "Reference.png"))
+    concat_img.save(os.path.join(output_dir, "Concat.pdf"), "PDF", resolution=100.0)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python annotating_with_checks.py <Dir>")
+        sys.exit(1)
+
+    root_dir = sys.argv[1]
+    results = annotating.make_dictionary(root_dir)
+
+
+    tasks = [(root_dir, sid, lbls) for sid, lbls in results.items()]
+
+    # print(tasks)
+
+    with concurrent.futures.ThreadPoolExecutor(max_workers=2) as executor:
+        executor.map(process_student, tasks)
diff --git a/reading_annotations.py b/reading_annotations.py
new file mode 100644
index 0000000..7fd7cc9
--- /dev/null
+++ b/reading_annotations.py
@@ -0,0 +1,325 @@
+import sys
+import os
+import json
+import numpy as np
+import shutil
+from PIL import Image, ImageChops
+Image.MAX_IMAGE_PIXELS = None
+from pdf2image import convert_from_path
+import annotating # Reuse rendering logic
+
+def detect_checks_and_notes(output_dir):
+    """
+    Returns:
+        actions: List of dicts {type, label, ...} for checked boxes
+        notes_img: RGBA image of manual notes (checks masked out)
+    """
+    pdf_path = os.path.join(output_dir, "Concat_annotated.pdf")
+    ref_path = os.path.join(output_dir, "Reference.png")
+    json_path = os.path.join(output_dir, "checkboxes.json")
+
+    if not (os.path.exists(pdf_path) and os.path.exists(ref_path)):
+        print(f"Missing files in {output_dir}")
+        return [], None
+
+    # Load Coordinates
+    with open(json_path, 'r') as f:
+        boxes = json.load(f)
+
+    # Load Reference
+    ref_img = Image.open(ref_path).convert("RGB")
+
+    # Load User PDF (First page only, assuming it's one long strip)
+    # Warning: If the PDF is huge, pdf2image might split pages or OOM.
+    # Assuming user didn't change page dimensions/order.
+    try:
+        user_pages = convert_from_path(pdf_path)
+    except Exception as e:
+        print(f"Error reading PDF: {e}")
+        return [], None
+    print("Debug : user_pages", len(user_pages))
+    # Concatenate PDF pages back to one image if user saved as multiple pages
+    # (Xournal++ might preserve the long format or split it)
+    total_h = sum(p.height for p in user_pages)
+    user_img = Image.new("RGB", (user_pages[0].width, total_h))
+    y = 0
+    for p in user_pages:
+        user_img.paste(p, (0, y))
+        y += p.height
+
+    # Resize user_img to match ref_img if slight mismatch (DPI export diffs)
+    if user_img.size != ref_img.size:
+        print("Debug : size mismatch : ", user_img.size, ref_img.size)
+        user_img = user_img.resize(ref_img.size, Image.Resampling.LANCZOS)
+
+    # --- Detection Phase ---
+    actions = []
+
+    # Convert to numpy for analysis
+    ref_arr = np.array(ref_img)
+    user_arr = np.array(user_img)
+
+    # Diff for analysis
+    # Simple absolute difference
+    diff = np.abs(ref_arr.astype(int) - user_arr.astype(int)).astype(np.uint8)
+    # Convert to grayscale for thresholding
+    diff_gray = np.mean(diff, axis=2)
+
+    # Threshold for "Checked"
+    CHECK_THRESHOLD = 30 # intensity diff
+    DENSITY_THRESHOLD = 0.05 # 5% of pixels darkened
+
+    # Mask to hide checkmarks from the "Notes" extraction
+    mask_img = Image.new("L", ref_img.size, 255) # White = keep, Black = hide
+    mask_draw = ImageDraw.Draw(mask_img)
+
+    for box in boxes:
+        # global_box: [x1, y1, x2, y2]
+        b = box['global_box']
+        x1, y1, x2, y2 = map(int, b)
+
+        # Ensure bounds
+        x1, y1 = max(0, x1), max(0, y1)
+        x2, y2 = min(ref_img.width, x2), min(ref_img.height, y2)
+
+        # Analyze ROI
+        roi = diff_gray[y1+5:y2-5, x1+5:x2-5]
+        if roi.size == 0: continue
+
+        changed_pixels = np.sum(roi > CHECK_THRESHOLD)
+        density = changed_pixels / roi.size
+
+        if density > DENSITY_THRESHOLD:
+            print("A checked box !", density, b)
+            actions.append(box)
+            # It's checked, so we mask this area out for manual notes
+            # Expand mask slightly to catch sloppy ticks
+            mask_draw.rectangle([x1-5, y1-5, x2+5, y2+5], fill=0)
+        else:
+            # print("A box, not checked !", density)
+            # Even if not "checked", mask the box area slightly to avoid
+            # artifacts if user hovered over it, though arguably we keep it.
+            # Let's strictly mask only if checked to verify detection?
+            # No, prompt says "not extract the part that are just checking".
+            # If user checked it, we mask it.
+            pass
+
+    # --- Extraction Phase ---
+    # Create the "Manual Notes" layer
+    # Logic: User - Ref. If Diff is dark -> Note.
+    # We want a transparent image with just the pen strokes.
+
+    # 1. Get difference image
+    diff_img = ImageChops.difference(ref_img, user_img).convert("L")
+
+    # 2. Threshold to remove JPEG noise (white background isn't perfect)
+    # Pixels that are different enough:
+    diff_data = np.array(diff_img)
+    # Create alpha channel: 0 where no diff, 255 where diff
+    alpha = np.where(diff_data > 20, 255, 0).astype(np.uint8)
+
+    # 3. Create output image (Black strokes, variable alpha)
+    # Or Copy user colors? Better to copy user pixels.
+    notes = user_img.convert("RGBA")
+    r, g, b, a = notes.split()
+
+    # Combine the diff-based alpha with the box-mask
+    mask_arr = np.array(mask_img)
+    final_alpha = np.minimum(alpha, mask_arr)
+
+    notes.putalpha(Image.fromarray(final_alpha))
+
+    return actions, notes
+
+from PIL import ImageDraw
+
+def apply_actions_and_regenerate(root_dir, data, student_id, actions, notes_layer):
+    """
+    Modifies data based on actions, calls annotating.process_correction logic,
+    overlays notes, saves Concat.jpg.
+    """
+    labels = data[student_id]
+
+    # 1. Apply Actions to Data
+    # Sort actions to handle indices correctly (delete from end?)
+    # But we regenerate from dictionary, so modifying the dictionary is fine.
+
+    # Separate actions by label
+    actions_by_label = {}
+    for a in actions:
+        l = a['label']
+        if l not in actions_by_label: actions_by_label[l] = []
+        actions_by_label[l].append(a)
+
+    for label, acts in actions_by_label.items():
+        if label not in labels: continue
+
+        content = labels[label]
+        result = content['result']
+        feedbacks = result.get('feedback', [])
+
+        # Split feedbacks again to match indices
+        global_fb_indices = [i for i, f in enumerate(feedbacks) if not f.get('box_2d')]
+        local_fb_indices = [i for i, f in enumerate(feedbacks) if f.get('box_2d')]
+        # Sort local by Y to match generation order in annotating.py
+        local_fb_sorted_map = sorted(local_fb_indices, key=lambda i: feedbacks[i]['box_2d'][0])
+
+        items_to_remove = set()
+
+        for act in acts:
+            if act['type'] == 'set_score':
+                result['score'] = act['value']
+                print(f"  > Updated score for {label} to {act['value']}")
+
+            elif act['type'] == 'del_global':
+                # act['index'] is the index within the global_fb list
+                # We need to find the actual index in the main list
+                if act['index'] < len(global_fb_indices):
+                    real_idx = global_fb_indices[act['index']]
+                    items_to_remove.add(real_idx)
+                    print(f"  > Deleted global feedback in {label}")
+
+            elif act['type'] == 'del_local':
+                # act['index'] is index in sorted local list
+                if act['index'] < len(local_fb_sorted_map):
+                    real_idx = local_fb_sorted_map[act['index']]
+                    items_to_remove.add(real_idx)
+                    print(f"  > Deleted local feedback in {label}")
+
+        # Remove feedbacks (in reverse to preserve indices)
+        for idx in sorted(list(items_to_remove), reverse=True):
+            del feedbacks[idx]
+
+    # 2. Regenerate Clean Image
+    # We use a temporary modified dictionary
+    temp_data = {student_id: labels}
+
+    # Run the original process (but we need to intercept it to not save, or just let it save)
+    # annotating.process_correction saves to "Anot_CopieID".
+    # We want "Bnot_CopieID" (updated).
+
+    # Hijack the output dir in logic or copy code?
+    # Easiest: Let's create a temporary helper or modify annotating logic slightly?
+    # The prompt implies we use `annotating.py` logic.
+    # Let's call `annotating.process_correction` but point it to a temp root or modify path?
+    # No, `process_correction` takes `root_dir` and writes to `Anot_...`.
+    # Let's just implement the rendering loop here to be safe and clean,
+    # overlaying the notes at the end.
+
+    output_dir = os.path.join(root_dir, "Bnot", f"Copie{student_id}")
+    # Don't delete output_dir, we need it.
+
+    # ... (Reuse rendering logic from annotating.py exactly) ...
+    # See below for condensed integration
+
+    final_concats = []
+
+    for label, content in labels.items():
+        # ... [PDF to Image Conversion] ...
+        copie_folder = f"Copie{student_id}"
+        pdf_path = os.path.join(root_dir, copie_folder, f"{label}.pdf")
+        if not os.path.exists(pdf_path): continue
+
+        pages = annotating.convert_from_path(pdf_path)
+        base_img = Image.new("RGBA", (max(p.width for p in pages), sum(p.height for p in pages)), "white")
+        y=0
+        for p in pages: base_img.paste(p.convert("RGBA"), (0,y)); y+=p.height
+
+        # ... [Draw Header/Margin (Clean)] ...
+        margin_left = 200
+        result = content['result']
+        coordinates = content.get('coordinates', (0,0))
+        hmin = coordinates[0]
+
+        score_text = f"{label}   ;   Note : {result.get('score', 0)}"
+        if result.get('error') and result.get('error') != "null": score_text += f" | Error: {result.get('error')}"
+
+        header_imgs = [annotating.render_latex_text(score_text, base_img.width, fontsize=18)]
+
+        feedbacks = result.get('feedback', [])
+        # Separate again (now cleaned)
+        global_fb = [f for f in feedbacks if not f.get('box_2d')]
+        local_fb = [f for f in feedbacks if f.get('box_2d')]
+        local_fb.sort(key=lambda x: x['box_2d'][0])
+
+        for fb in global_fb: header_imgs.append(annotating.render_latex_text(fb['text'], base_img.width))
+
+        total_h = base_img.height + sum(i.height for i in header_imgs)
+        label_img = Image.new("RGB", (base_img.width + margin_left, total_h), "white")
+
+        cy = 0
+        for i in header_imgs: label_img.paste(i, (0, cy)); cy+=i.height
+        img_offset_y = cy
+        label_img.paste(base_img, (margin_left, img_offset_y))
+
+        draw = ImageDraw.Draw(label_img, "RGBA")
+        last_bot = 0
+        for fb in local_fb:
+            box = fb['box_2d']
+            ymin, xmin, ymax, xmax = box
+            t_ymin = (ymin - hmin) + img_offset_y
+            t_ymax = (ymax - hmin) + img_offset_y
+            draw.rectangle([xmin+margin_left, t_ymin, xmax+margin_left, t_ymax], outline="red", width=3)
+
+            txt = annotating.render_latex_text(fb['text'], 500, (255,200,200,180), max_lines=3)
+            py = max((t_ymin+t_ymax)/2 - txt.height/2, img_offset_y)
+            if py < last_bot: py = last_bot + 5
+
+            if py + txt.height + 20 > label_img.height:
+                new_l = Image.new("RGB", (label_img.width, int(py+txt.height+20)), "white")
+                new_l.paste(label_img, (0,0))
+                label_img = new_l
+                draw = ImageDraw.Draw(label_img, "RGBA")
+
+            label_img.paste(txt, (10, int(py)), mask=txt)
+            last_bot = py + txt.height
+
+        final_concats.append(label_img)
+
+    # Concatenate Labels
+    if not final_concats: return
+
+    mw = max(i.width for i in final_concats)
+    th = sum(i.height for i in final_concats)
+    full_clean_img = Image.new("RGB", (mw, th), "white")
+    y=0
+    for i in final_concats:
+        full_clean_img.paste(i, (0,y))
+        y+=i.height
+
+    # 3. Overlay Manual Notes
+    if notes_layer:
+        # Notes layer might be different size if regenerated image size changed (e.g. deleted comments reduced height)
+        # However, usually reducing content reduces height, so we align top-left.
+        # But `notes_layer` is based on the "Reference.png" which had boxes.
+        # The new `full_clean_img` does NOT have boxes. The dimensions should be identical
+        # unless removing a feedback at the very bottom shrinks the image.
+
+        # We paste notes_layer on top.
+        full_clean_img.paste(notes_layer, (0,0), mask=notes_layer)
+
+    # Save final Concat.jpg
+    final_path = os.path.join(output_dir, "Concat.jpg")
+    full_clean_img.save(final_path)
+    print(f"Saved regenerated: {final_path}")
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python reading_annotations.py <Dir>")
+        sys.exit(1)
+
+    root_dir = sys.argv[1]
+
+    # Load original data
+    original_data = annotating.make_dictionary(root_dir)
+
+    # Process each Bnot folder
+    for student_id in original_data.keys():
+        bnot_dir = os.path.join(root_dir, "Bnot", f"Copie{student_id}")
+        if os.path.exists(bnot_dir):
+            print(f"Processing annotations for: {student_id}")
+            actions, notes = detect_checks_and_notes(bnot_dir)
+            if actions or notes:
+                apply_actions_and_regenerate(root_dir, original_data, student_id, actions, notes)
+            else:
+                print("  No changes detected or missing files.")