diff --git a/pageindex/__init__.py b/pageindex/__init__.py
index f8a75d5..4606eb3 100644
--- a/pageindex/__init__.py
+++ b/pageindex/__init__.py
@@ -1 +1,2 @@
-from .page_index import *
\ No newline at end of file
+from .page_index import *
+from .page_index_md import md_to_tree
\ No newline at end of file
diff --git a/pageindex/page_index_md.py b/pageindex/page_index_md.py
new file mode 100644
index 0000000..be5949d
--- /dev/null
+++ b/pageindex/page_index_md.py
@@ -0,0 +1,288 @@
+import asyncio
+import json
+import re
+from .utils import *
+
+
+async def get_node_summary(node, summary_token_threshold=200, model=None):
+    node_text = node.get('text')
+    num_tokens = count_tokens(node_text, model=model)
+    if num_tokens < summary_token_threshold:
+        return node_text
+    else:
+        return await generate_node_summary(node, model=model)
+
+
+async def generate_summaries_for_structure_md(structure, summary_token_threshold, model=None):
+    nodes = structure_to_list(structure)
+    tasks = [get_node_summary(node, summary_token_threshold=summary_token_threshold, model=model) for node in nodes]
+    summaries = await asyncio.gather(*tasks)
+    
+    for node, summary in zip(nodes, summaries):
+        if not node.get('nodes'):
+            node['summary'] = summary
+        else:
+            node['prefix_summary'] = summary
+    return structure
+
+
+def extract_nodes_from_markdown(markdown_content):
+    header_pattern = r'^(#{1,6})\s+(.+)$'
+    node_list = []
+    
+    lines = markdown_content.split('\n')
+    for line_num, line in enumerate(lines, 1):
+        line = line.strip()
+        if not line:
+            continue
+            
+        match = re.match(header_pattern, line)
+        if match:
+            title = match.group(2).strip()
+            node_list.append({'node_title': title, 'line_num': line_num})
+
+    return node_list,lines
+
+
+def extract_node_text_content(node_list, markdown_lines):    
+    all_nodes = []
+    for node in node_list:
+        processed_node = {
+            'title': node['node_title'],
+            'line_num': node['line_num'],
+            'level': len(re.match(r'^(#{1,6})', markdown_lines[node['line_num'] - 1]).group(1))
+        }
+        all_nodes.append(processed_node)
+    
+    for i, node in enumerate(all_nodes):
+        start_line = node['line_num'] - 1 
+        if i + 1 < len(all_nodes):
+            end_line = all_nodes[i + 1]['line_num'] - 1 
+        else:
+            end_line = len(markdown_lines)
+        
+        node['text'] = '\n'.join(markdown_lines[start_line:end_line]).strip()    
+    return all_nodes
+
+def update_node_list_with_text_token_count(node_list, model=None):
+
+    def find_all_children(parent_index, parent_level, node_list):
+        """Find all direct and indirect children of a parent node"""
+        children_indices = []
+        
+        # Look for children after the parent
+        for i in range(parent_index + 1, len(node_list)):
+            current_level = node_list[i]['level']
+            
+            # If we hit a node at same or higher level than parent, stop
+            if current_level <= parent_level:
+                break
+                
+            # This is a descendant
+            children_indices.append(i)
+        
+        return children_indices
+    
+    # Make a copy to avoid modifying the original
+    result_list = node_list.copy()
+    
+    # Process nodes from end to beginning to ensure children are processed before parents
+    for i in range(len(result_list) - 1, -1, -1):
+        current_node = result_list[i]
+        current_level = current_node['level']
+        
+        # Get all children of this node
+        children_indices = find_all_children(i, current_level, result_list)
+        
+        # Start with the node's own text
+        node_text = current_node.get('text', '')
+        total_text = node_text
+        
+        # Add all children's text
+        for child_index in children_indices:
+            child_text = result_list[child_index].get('text', '')
+            if child_text:
+                total_text += '\n' + child_text
+        
+        # Calculate token count for combined text
+        result_list[i]['text_token_count'] = count_tokens(total_text, model=model)
+    
+    return result_list
+
+
+def tree_thinning_for_index(node_list, min_node_token=None, model=None):
+    def find_all_children(parent_index, parent_level, node_list):
+        children_indices = []
+        
+        for i in range(parent_index + 1, len(node_list)):
+            current_level = node_list[i]['level']
+            
+            if current_level <= parent_level:
+                break
+                
+            children_indices.append(i)
+        
+        return children_indices
+    
+    result_list = node_list.copy()
+    nodes_to_remove = set()
+    
+    for i in range(len(result_list) - 1, -1, -1):
+        if i in nodes_to_remove:
+            continue
+            
+        current_node = result_list[i]
+        current_level = current_node['level']
+        
+        total_tokens = current_node.get('text_token_count', 0)
+        
+        if total_tokens < min_node_token:
+            children_indices = find_all_children(i, current_level, result_list)
+            
+            children_texts = []
+            for child_index in sorted(children_indices):
+                if child_index not in nodes_to_remove:
+                    child_text = result_list[child_index].get('text', '')
+                    if child_text.strip():
+                        children_texts.append(child_text)
+                    nodes_to_remove.add(child_index)
+            
+            if children_texts:
+                parent_text = current_node.get('text', '')
+                merged_text = parent_text
+                for child_text in children_texts:
+                    if merged_text and not merged_text.endswith('\n'):
+                        merged_text += '\n\n'
+                    merged_text += child_text
+                
+                result_list[i]['text'] = merged_text
+                
+                result_list[i]['text_token_count'] = count_tokens(merged_text, model=model)
+    
+    for index in sorted(nodes_to_remove, reverse=True):
+        result_list.pop(index)
+    
+    return result_list
+
+
+def build_tree_from_nodes(node_list):
+    if not node_list:
+        return []
+    
+    stack = []
+    root_nodes = []
+    node_counter = 1
+    
+    for node in node_list:
+        current_level = node['level']
+        
+        tree_node = {
+            'title': node['title'],
+            'node_id': str(node_counter).zfill(4),
+            'text': node['text'],
+            'line_num': node['line_num'],
+            'nodes': []
+        }
+        node_counter += 1
+        
+        while stack and stack[-1][1] >= current_level:
+            stack.pop()
+        
+        if not stack:
+            root_nodes.append(tree_node)
+        else:
+            parent_node, parent_level = stack[-1]
+            parent_node['nodes'].append(tree_node)
+        
+        stack.append((tree_node, current_level))
+    
+    return root_nodes
+
+
+def clean_tree_for_output(tree_nodes):
+    cleaned_nodes = []
+    
+    for node in tree_nodes:
+        cleaned_node = {
+            'title': node['title'],
+            'node_id': node['node_id'],
+            'text': node['text'],
+            'line_num': node['line_num']
+        }
+        
+        if node['nodes']:
+            cleaned_node['nodes'] = clean_tree_for_output(node['nodes'])
+        
+        cleaned_nodes.append(cleaned_node)
+    
+    return cleaned_nodes
+
+
+async def md_to_tree(md_path, if_thinning=True, min_token_threshold=None, if_summary=True, summary_token_threshold=None, model=None):
+    with open(md_path, 'r', encoding='utf-8') as f:
+        markdown_content = f.read()
+    
+    print(f"Extracting nodes from markdown...")
+    node_list, markdown_lines = extract_nodes_from_markdown(markdown_content)
+
+    print(f"Extracting text content from nodes...")
+    nodes_with_content = extract_node_text_content(node_list, markdown_lines)
+    
+    if if_thinning:
+        nodes_with_content = update_node_list_with_text_token_count(nodes_with_content, model=model)
+        print(f"Thinning nodes...")
+        nodes_with_content = tree_thinning_for_index(nodes_with_content, min_token_threshold, model=model)
+    
+    print(f"Building tree from nodes...")
+    tree_structure = build_tree_from_nodes(nodes_with_content)
+
+    if if_summary:
+        print(f"Generating summaries for each node...")
+        tree_structure = await generate_summaries_for_structure_md(tree_structure,summary_token_threshold=summary_token_threshold, model=model)
+
+    print(f"Formatting tree structure...")
+    tree_structure = format_structure(tree_structure, order = ['title', 'node_id', 'summary', 'prefix_summary', 'text', 'line_num', 'nodes'])
+    
+    return tree_structure
+
+
+if __name__ == "__main__":
+    import os
+    import json
+    
+    MD_NAME = 'Detect-Order-Construct'
+    # MD_NAME = 'Welcome'
+    MD_PATH = os.path.join(os.path.dirname(__file__), '..', 'docs', f'{MD_NAME}.md')
+
+
+    MODEL="gpt-4.1"
+    IF_THINNING=False
+    THINNING_THRESHOLD=5000
+    SUMMARY_TOKEN_THRESHOLD=200
+    IF_SUMMARY=True
+
+    tree_structure = asyncio.run(md_to_tree(
+        md_path=MD_PATH, 
+        if_thinning=IF_THINNING, 
+        min_token_threshold=THINNING_THRESHOLD, 
+        if_summary=IF_SUMMARY, 
+        summary_token_threshold=SUMMARY_TOKEN_THRESHOLD, 
+        model=MODEL))
+    
+    print('\n' + '='*60)
+    print('TREE STRUCTURE')
+    print('='*60)
+    print_json(tree_structure)
+
+    print('\n' + '='*60)
+    print('TABLE OF CONTENTS')
+    print('='*60)
+    print_toc(tree_structure)
+
+    output_path = os.path.join(os.path.dirname(__file__), '..', 'results', f'{MD_NAME}_structure.json')
+    os.makedirs(os.path.dirname(output_path), exist_ok=True)
+    
+    with open(output_path, 'w', encoding='utf-8') as f:
+        json.dump(tree_structure, f, indent=2, ensure_ascii=False)
+    
+    print(f"\nTree structure saved to: {output_path}")
\ No newline at end of file
diff --git a/pageindex/utils.py b/pageindex/utils.py
index e25a534..db29ce8 100644
--- a/pageindex/utils.py
+++ b/pageindex/utils.py
@@ -19,8 +19,9 @@ from types import SimpleNamespace as config
 
 CHATGPT_API_KEY = os.getenv("CHATGPT_API_KEY")
 
-
-def count_tokens(text, model):
+def count_tokens(text, model=None):
+    if not text:
+        return 0
     enc = tiktoken.encoding_for_model(model)
     tokens = enc.encode(text)
     return len(tokens)
@@ -489,6 +490,34 @@ def clean_structure_post(data):
             clean_structure_post(section)
     return data
 
+def remove_fields(data, fields=['text']):
+    if isinstance(data, dict):
+        return {k: remove_fields(v, fields)
+            for k, v in data.items() if k not in fields}
+    elif isinstance(data, list):
+        return [remove_fields(item, fields) for item in data]
+    return data
+
+def print_toc(tree, indent=0):
+    for node in tree:
+        print('  ' * indent + node['title'])
+        if node.get('nodes'):
+            print_toc(node['nodes'], indent + 1)
+
+def print_json(data, max_len=40, indent=2):
+    def simplify_data(obj):
+        if isinstance(obj, dict):
+            return {k: simplify_data(v) for k, v in obj.items()}
+        elif isinstance(obj, list):
+            return [simplify_data(item) for item in obj]
+        elif isinstance(obj, str) and len(obj) > max_len:
+            return obj[:max_len] + '...'
+        else:
+            return obj
+    
+    simplified = simplify_data(data)
+    print(json.dumps(simplified, indent=indent, ensure_ascii=False))
+
 
 def remove_structure_text(data):
     if isinstance(data, dict):
@@ -606,6 +635,26 @@ def generate_doc_description(structure, model=None):
     return response
 
 
+def reorder_dict(data, key_order):
+    if not key_order:
+        return data
+    return {key: data[key] for key in key_order if key in data}
+
+
+def format_structure(structure, order=None):
+    if not order:
+        return structure
+    if isinstance(structure, dict):
+        if 'nodes' in structure:
+            structure['nodes'] = format_structure(structure['nodes'], order)
+        if not structure.get('nodes'):
+            structure.pop('nodes', None)
+        structure = reorder_dict(structure, order)
+    elif isinstance(structure, list):
+        structure = [format_structure(item, order) for item in structure]
+    return structure
+
+
 class ConfigLoader:
     def __init__(self, default_path: str = None):
         if default_path is None:
diff --git a/requirements.txt b/requirements.txt
index ad43fe1..463db58 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
-openai==1.70.0
-pymupdf==1.25.5
+openai==1.101.0
+pymupdf==1.26.4
 PyPDF2==3.0.1
 python-dotenv==1.1.0
-tiktoken==0.7.0
+tiktoken==0.11.0
 pyyaml==6.0.2
diff --git a/run_pageindex.py b/run_pageindex.py
index 63b2206..2a9f29a 100644
--- a/run_pageindex.py
+++ b/run_pageindex.py
@@ -1,17 +1,22 @@
 import argparse
+import os
+import json
 from pageindex import *
+from pageindex.page_index_md import md_to_tree
 
 if __name__ == "__main__":
     # Set up argument parser
-    parser = argparse.ArgumentParser(description='Process PDF document and generate structure')
-    parser.add_argument('--pdf_path', type=str, help='Path to the PDF file')
+    parser = argparse.ArgumentParser(description='Process PDF or Markdown document and generate structure')
+    parser.add_argument('--file_path', type=str, help='Path to the PDF or Markdown file')
+    parser.add_argument('--file_type', type=str, choices=['pdf', 'markdown', 'md'], default='pdf',
+                      help='Type of file to process (pdf, markdown, or md)')
     parser.add_argument('--model', type=str, default='gpt-4o-2024-11-20', help='Model to use')
     parser.add_argument('--toc-check-pages', type=int, default=20, 
-                      help='Number of pages to check for table of contents')
+                      help='Number of pages to check for table of contents (PDF only)')
     parser.add_argument('--max-pages-per-node', type=int, default=10,
-                      help='Maximum number of pages per node')
+                      help='Maximum number of pages per node (PDF only)')
     parser.add_argument('--max-tokens-per-node', type=int, default=20000,
-                      help='Maximum number of tokens per node')
+                      help='Maximum number of tokens per node (PDF only)')
     parser.add_argument('--if-add-node-id', type=str, default='yes',
                       help='Whether to add node id to the node')
     parser.add_argument('--if-add-node-summary', type=str, default='no',
@@ -20,27 +25,73 @@ if __name__ == "__main__":
                       help='Whether to add doc description to the doc')
     parser.add_argument('--if-add-node-text', type=str, default='no',
                       help='Whether to add text to the node')
+    # Markdown specific arguments
+    parser.add_argument('--if-thinning', type=str, default='yes',
+                      help='Whether to apply tree thinning for markdown (markdown only)')
+    parser.add_argument('--thinning-threshold', type=int, default=5000,
+                      help='Minimum token threshold for thinning (markdown only)')
+    parser.add_argument('--summary-token-threshold', type=int, default=200,
+                      help='Token threshold for generating summaries (markdown only)')
     args = parser.parse_args()
-        
+    
+    # Determine file type from extension if not specified
+    if args.file_type == 'pdf' and args.file_path:
+        if args.file_path.lower().endswith(('.md', '.markdown')):
+            args.file_type = 'markdown'
+        elif not args.file_path.lower().endswith('.pdf'):
+            raise ValueError("File must be a PDF or Markdown file")
+    
+    if args.file_type == 'pdf':
+        # Process PDF file
         # Configure options
-    opt = config(
-        model=args.model,
-        toc_check_page_num=args.toc_check_pages,
-        max_page_num_each_node=args.max_pages_per_node,
-        max_token_num_each_node=args.max_tokens_per_node,
-        if_add_node_id=args.if_add_node_id,
-        if_add_node_summary=args.if_add_node_summary,
-        if_add_doc_description=args.if_add_doc_description,
-        if_add_node_text=args.if_add_node_text
-    )
+        opt = config(
+            model=args.model,
+            toc_check_page_num=args.toc_check_pages,
+            max_page_num_each_node=args.max_pages_per_node,
+            max_token_num_each_node=args.max_tokens_per_node,
+            if_add_node_id=args.if_add_node_id,
+            if_add_node_summary=args.if_add_node_summary,
+            if_add_doc_description=args.if_add_doc_description,
+            if_add_node_text=args.if_add_node_text
+        )
 
-    # Process the PDF
-    toc_with_page_number = page_index_main(args.pdf_path, opt)
-    print('Parsing done, saving to file...')
-    
-    # Save results
-    pdf_name = os.path.splitext(os.path.basename(args.pdf_path))[0]    
-    os.makedirs('./results', exist_ok=True)
-    
-    with open(f'./results/{pdf_name}_structure.json', 'w', encoding='utf-8') as f:
-        json.dump(toc_with_page_number, f, indent=2)
\ No newline at end of file
+        # Process the PDF
+        toc_with_page_number = page_index_main(args.file_path, opt)
+        print('Parsing done, saving to file...')
+        
+        # Save results
+        pdf_name = os.path.splitext(os.path.basename(args.file_path))[0]    
+        os.makedirs('./results', exist_ok=True)
+        
+        with open(f'./results/{pdf_name}_structure.json', 'w', encoding='utf-8') as f:
+            json.dump(toc_with_page_number, f, indent=2)
+            
+    elif args.file_type in ['markdown', 'md']:
+        # Process markdown file
+        print('Processing markdown file...')
+        
+        # Configure markdown options
+        if_thinning = args.if_thinning.lower() == 'yes'
+        if_summary = args.if_add_node_summary.lower() == 'yes'
+        
+        # Process the markdown
+        import asyncio
+        toc_with_page_number = asyncio.run(md_to_tree(
+            md_path=args.file_path,
+            if_thinning=if_thinning,
+            min_token_threshold=args.thinning_threshold,
+            if_summary=if_summary,
+            summary_token_threshold=args.summary_token_threshold,
+            model=args.model
+        ))
+        
+        print('Parsing done, saving to file...')
+        
+        # Save results
+        md_name = os.path.splitext(os.path.basename(args.file_path))[0]    
+        os.makedirs('./results', exist_ok=True)
+        
+        with open(f'./results/{md_name}_structure.json', 'w', encoding='utf-8') as f:
+            json.dump(toc_with_page_number, f, indent=2, ensure_ascii=False)
+    else:
+        raise ValueError(f"Unsupported file type: {args.file_type}. Supported types are 'pdf', 'markdown', or 'md'")
\ No newline at end of file