diff --git a/MANIFEST.in b/MANIFEST.in
index 9af3705..2a0ae03 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1 +1,2 @@
 include environments/*
+include apps/*
diff --git a/bioengine/services/cellpose/README.md b/apps/cellpose/README.md
similarity index 100%
rename from bioengine/services/cellpose/README.md
rename to apps/cellpose/README.md
diff --git a/bioengine/services/cellpose/predict/1/model.py b/apps/cellpose/cellpose-predict/1/model.py
similarity index 100%
rename from bioengine/services/cellpose/predict/1/model.py
rename to apps/cellpose/cellpose-predict/1/model.py
diff --git a/bioengine/services/cellpose/predict/1/pyodide_test.py b/apps/cellpose/cellpose-predict/1/pyodide_test.py
similarity index 100%
rename from bioengine/services/cellpose/predict/1/pyodide_test.py
rename to apps/cellpose/cellpose-predict/1/pyodide_test.py
diff --git a/bioengine/services/cellpose/predict/config.pbtxt b/apps/cellpose/cellpose-predict/config.pbtxt
similarity index 100%
rename from bioengine/services/cellpose/predict/config.pbtxt
rename to apps/cellpose/cellpose-predict/config.pbtxt
diff --git a/bioengine/services/cellpose/train/1/build_bioimageio_package.py b/apps/cellpose/cellpose-train/1/build_bioimageio_package.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/build_bioimageio_package.py
rename to apps/cellpose/cellpose-train/1/build_bioimageio_package.py
diff --git a/bioengine/services/cellpose/train/1/interactive_cellpose.py b/apps/cellpose/cellpose-train/1/interactive_cellpose.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/interactive_cellpose.py
rename to apps/cellpose/cellpose-train/1/interactive_cellpose.py
diff --git a/bioengine/services/cellpose/train/1/model.py b/apps/cellpose/cellpose-train/1/model.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/model.py
rename to apps/cellpose/cellpose-train/1/model.py
diff --git a/bioengine/services/cellpose/train/1/predict.py b/apps/cellpose/cellpose-train/1/predict.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/predict.py
rename to apps/cellpose/cellpose-train/1/predict.py
diff --git a/bioengine/services/cellpose/train/1/test_cellpose_train.py b/apps/cellpose/cellpose-train/1/test_cellpose_train.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/test_cellpose_train.py
rename to apps/cellpose/cellpose-train/1/test_cellpose_train.py
diff --git a/bioengine/services/cellpose/train/1/test_native.py b/apps/cellpose/cellpose-train/1/test_native.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/test_native.py
rename to apps/cellpose/cellpose-train/1/test_native.py
diff --git a/bioengine/services/cellpose/train/1/test_triton.py b/apps/cellpose/cellpose-train/1/test_triton.py
similarity index 100%
rename from bioengine/services/cellpose/train/1/test_triton.py
rename to apps/cellpose/cellpose-train/1/test_triton.py
diff --git a/bioengine/services/cellpose/train/config.pbtxt b/apps/cellpose/cellpose-train/config.pbtxt
similarity index 100%
rename from bioengine/services/cellpose/train/config.pbtxt
rename to apps/cellpose/cellpose-train/config.pbtxt
diff --git a/apps/cellpose/main.py b/apps/cellpose/main.py
new file mode 100644
index 0000000..6b619d2
--- /dev/null
+++ b/apps/cellpose/main.py
@@ -0,0 +1,42 @@
+from hypha_launcher.utils.container import ContainerEngine
+from pathlib import Path
+from pyotritonclient import get_config, execute
+from functools import partial
+import logging
+
+logger = logging.getLogger(__name__)
+
+container_engine = ContainerEngine()
+TRITON_IMAGE = "docker://nvcr.io/nvidia/tritonserver:23.03-py3"
+
+
+async def hypha_startup(server):
+    # get current dir
+    current_dir = Path(__file__).parent
+    host_port = "9302"
+    logger.info(f"Pulling triton image {TRITON_IMAGE}")
+    container_engine.pull_image(TRITON_IMAGE)
+    logger.info(f"Starting triton server at port {host_port}")
+    container_engine.run_command(
+        f'bash -c "tritonserver --model-repository=/models --log-verbose=3 --log-info=1 --log-warning=1 --log-error=1 --model-control-mode=poll --exit-on-error=false --repository-poll-secs=10 --allow-grpc=False --http-port={host_port}"',  # noqa
+        TRITON_IMAGE,
+        ports={host_port: host_port},
+        volumes={str(current_dir): "/models"},
+    )
+    
+    server_url = f"http://localhost:{host_port}"
+    logger.info(f"Triton server is running at {server_url}")
+
+    svc = await server.register_service({
+        "name": "CellPose",
+        "id": "cellpose",
+        "config": {
+            "visibility": "public"
+        },
+        "train": partial(execute, server_url=server_url, model_name="cellpose-train"),
+        "train_config": partial(get_config, server_url=server_url, model_name="cellpose-train"),
+        "predict": partial(execute, server_url=server_url, model_name="cellpose-predict"),
+        "predict_config": partial(get_config, server_url=server_url, model_name="cellpose-predict"),
+    })
+    
+    logger.info(f"CellPose service is registered as `{svc['id']}`")
\ No newline at end of file
diff --git a/apps/cellpose/manifest.yaml b/apps/cellpose/manifest.yaml
new file mode 100644
index 0000000..d3e169c
--- /dev/null
+++ b/apps/cellpose/manifest.yaml
@@ -0,0 +1,5 @@
+name: Cellpose
+id: cellpose
+description: Cellpose is a generalist algorithm for cell and nucleus segmentation
+runtime: python
+entrypoint: main.py
diff --git a/apps/imagej/main.py b/apps/imagej/main.py
new file mode 100644
index 0000000..11fac1b
--- /dev/null
+++ b/apps/imagej/main.py
@@ -0,0 +1,228 @@
+import logging
+import sys, os
+import imagej
+import scyjava as sj
+import asyncio
+import traceback
+import numpy as np
+import xarray as xr
+from jpype import JOverride, JImplements
+
+
+logger = logging.getLogger(__name__)
+os.environ["JAVA_HOME"] = os.sep.join(sys.executable.split(os.sep)[:-2] + ["jre"])
+
+def capture_console(ij, print=True):
+    logs = {}
+    logs["stdout"] = []
+    logs["stderr"] = []
+
+    @JImplements("org.scijava.console.OutputListener")
+    class JavaOutputListener:
+        @JOverride
+        def outputOccurred(self, e):
+            source = e.getSource().toString
+            output = e.getOutput()
+
+            if print:
+                if source == "STDOUT":
+                    sys.stdout.write(output)
+                    logs["stdout"].append(output)
+                elif source == "STDERR":
+                    sys.stderr.write(output)
+                    logs["stderr"].append(output)
+                else:
+                    output = "[{}] {}".format(source, output)
+                    sys.stderr.write(output)
+                    logs["stderr"].append(output)
+
+    ij.py._outputMapper = JavaOutputListener()
+    ij.console().addOutputListener(ij.py._outputMapper)
+    return logs
+
+
+def format_logs(logs):
+    output = ""
+    if logs["stdout"]:
+        output += "STDOUT:\n"
+        output += "\n".join(logs["stdout"])
+        output += "\n"
+    if logs["stderr"]:
+        output += "STDERR:\n"
+        output += "\n".join(logs["stderr"])
+        output += "\n"
+    return output
+
+
+def get_module_info(ij, custom_script, name=None):
+    name = name or "scijava_script"
+    ScriptInfo = sj.jimport("org.scijava.script.ScriptInfo")
+    StringReader = sj.jimport("java.io.StringReader")
+    moduleinfo = ScriptInfo(ij.getContext(), name, StringReader(custom_script))
+    inputs = {}
+    outputs = {}
+
+    for inp in ij.py.from_java(moduleinfo.inputs()):
+        input_type = str(inp.getType().getName())
+        input_name = str(inp.getName())
+        print(input_type, input_name)
+        inputs[input_name] = {"name": input_name, "type": input_type}
+
+    for outp in ij.py.from_java(moduleinfo.outputs()):
+        output_type = str(outp.getType().getName())
+        output_name = str(outp.getName())
+        outputs[output_name] = {"name": output_name, "type": output_type}
+
+    return {"id": moduleinfo.getIdentifier(), "outputs": outputs, "inputs": inputs}
+
+
+def check_size(array):
+    result_bytes = array.tobytes()
+    if len(result_bytes) > 20000000:  # 20MB
+        raise Exception(
+            f"The data is too large ({len(result_bytes)} bytes) to be transfered."
+        )
+
+
+async def execute(config, context=None):
+    loop = asyncio.get_event_loop()
+    return await loop.run_in_executor(None, run_imagej, config)
+
+
+def run_imagej(config):
+    headless = config.get("headless", False)
+    ij = imagej.init(os.environ["IMAGEJ_DIR"], headless=headless)
+    try:
+        WindowManager = sj.jimport("ij.WindowManager")
+        ImagePlus = sj.jimport("ij.ImagePlus")
+        logs = capture_console(ij)
+        script = config.get("script")
+        lang = config.get("lang", "ijm")
+        assert script is not None, "script is required"
+        module_info = get_module_info(ij, script)
+        inputs_info = module_info["inputs"]
+        outputs_info = module_info["outputs"]
+        inputs = config.get("inputs", {})
+        select_outputs = config.get("select_outputs")
+        args = {}
+        for k in inputs:
+            if isinstance(inputs[k], (np.ndarray, np.generic, dict)):
+                if isinstance(inputs[k], (np.ndarray, np.generic)):
+                    if inputs[k].ndim == 2:
+                        dims = ["x", "y"]
+                    elif inputs[k].ndim == 3 and inputs[k].shape[2] in [1, 3, 4]:
+                        dims = ["x", "y", "c"]
+                    elif inputs[k].ndim == 3 and inputs[k].shape[0] in [1, 3, 4]:
+                        dims = ["c", "x", "y"]
+                    elif inputs[k].ndim == 3:
+                        dims = ["z", "x", "y"]
+                    elif inputs[k].ndim == 4:
+                        dims = ["z", "x", "y", "c"]
+                    elif inputs[k].ndim == 5:
+                        dims = ["t", "z", "x", "y", "c"]
+                    else:
+                        raise Exception(f"Unsupported ndim: {inputs[k].ndim}")
+                    inputs[k] = {"data": inputs[k], "dims": dims}
+
+                img = inputs[k]
+                assert isinstance(
+                    img, dict
+                ), f"input {k} must be a dictionary or a numpy array"
+                assert "data" in img, f"data is required for {k}"
+                assert "dims" in img, f"dims is required for {k}"
+                da = xr.DataArray(
+                    data=img["data"],
+                    dims=img["dims"],
+                    attrs=img.get("attrs", {}),
+                    name=k,
+                )
+                inputs[k] = ij.py.to_java(da)
+                if lang == "ijm":
+                    # convert to ImagePlus
+                    inputs[k] = ij.convert().convert(inputs[k], ImagePlus)
+                    if inputs[k]:
+                        inputs[k].setTitle(k)
+                        # Display the image
+                        if not headless:
+                            inputs[k].show()
+                else:
+                    raise NotImplementedError(
+                        "Don't know how to display the image (only ijm is supported)."
+                    )
+            if k in inputs_info:
+                args[k] = ij.py.to_java(inputs[k])
+
+        # Run the script
+        macro_result = ij.py.run_script(lang, script, args)
+        results = {}
+        if select_outputs is None:
+            select_outputs = list(outputs_info.keys())
+        for k in select_outputs:
+            if k in outputs_info:
+                results[k] = macro_result.getOutput(k)
+                if results[k] and not isinstance(results[k], (int, str, float, bool)):
+                    try:
+                        results[k] = ij.py.from_java(results[k]).to_numpy()
+                        check_size(results[k])
+                    except Exception:
+                        # TODO: This is needed due to a bug in pyimagej for converting java string
+                        if str(type(results[k])) == "<java class 'java.lang.String'>":
+                            results[k] = str(results[k])
+                        else:
+                            results[k] = {
+                                "type": str(type(results[k])),
+                                "text": str(results[k]),
+                            }
+            else:
+                # If the output name is not in the script annotation,
+                # Try to get the image from the WindowManager by title
+                img = WindowManager.getImage(k)
+                if not img:
+                    raise Exception(f"Output not found: {k}\n{format_logs(logs)}")
+                results[k] = ij.py.from_java(img).to_numpy()
+                check_size(results[k])
+    except Exception as exp:
+        raise exp
+    finally:
+        ij.dispose()
+
+    return {"outputs": results, "logs": logs}
+
+
+
+test_macro = """
+#@ String name
+#@ int age
+#@ String city
+#@output Object greeting
+greeting = "Hi " + name + ". You are " + age + " years old, and live in " + city + "."
+"""
+
+async def hypha_startup(server):
+    try:
+        print("Testing the imagej service...")
+        ret = await execute(
+            {
+                "script": test_macro,
+                "inputs": {"name": "Tom", "age": 20, "city": "Shanghai"},
+            }
+        )
+        outputs = ret["outputs"]
+        assert (
+            outputs["greeting"] == "Hi Tom. You are 20 years old, and live in Shanghai."
+        )
+    except Exception:
+        print(traceback.format_exc())
+        sys.exit(1)
+
+    logger.info("Starting the imagej service...")
+    svc = await server.register_service(
+        {
+            "id": "imagej-service",
+            "type": "imagej-service",
+            "config": {"require_context": True, "visibility": "public"},
+            "execute": execute,
+        }
+    )
+    
+    logger.info(f"ImageJ service is registered as `{svc['id']}`")
\ No newline at end of file
diff --git a/apps/imagej/manifest.yaml b/apps/imagej/manifest.yaml
new file mode 100644
index 0000000..f0e025f
--- /dev/null
+++ b/apps/imagej/manifest.yaml
@@ -0,0 +1,5 @@
+name: ImageJ
+id: imagej
+description: ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
+runtime: conda
+entrypoint: main.py
diff --git a/bioengine/__init__.py b/bioengine/__init__.py
index 1814276..3202f6a 100644
--- a/bioengine/__init__.py
+++ b/bioengine/__init__.py
@@ -1,6 +1,13 @@
+from bioengine.app_loader import load_apps
+import logging
+
+logger = logging.getLogger(__name__)
 
 def connect_server(server_url):
     raise NotImplementedError("This function is not implemented yet.")
 
-def register_bioengine(server):
-    raise NotImplementedError("This function is not implemented yet.")
\ No newline at end of file
+async def register_bioengine_apps(server):
+    for app in load_apps():
+        logger.info(f"Registering service {app.name}")
+        await app.run(server)
+        logger.info(f"Service {app.name} registered.")
diff --git a/bioengine/__main__.py b/bioengine/__main__.py
index 4527e31..6f51a0a 100644
--- a/bioengine/__main__.py
+++ b/bioengine/__main__.py
@@ -2,11 +2,11 @@
 import argparse
 import asyncio
 import subprocess
-import os
+# import os
 
 def start_server(args):
     # get current file path so we can get the path of apps under the same directory
-    current_dir = os.path.dirname(os.path.abspath(__file__))
+    # current_dir = os.path.dirname(os.path.abspath(__file__))
     command = [
         sys.executable,
         "-m",
@@ -14,14 +14,12 @@ def start_server(args):
         f"--host={args.host}",
         f"--port={args.port}",
         f"--public-base-url={args.public_base_url}",
-        "--startup-functions=bioengine:register_bioengine"
+        "--startup-functions=bioengine:register_bioengine_apps"
     ]
     subprocess.run(command)
 
 def connect_server(args):
     from bioengine import connect_server
-    if args.login_required:
-        os.environ["BIOIMAGEIO_LOGIN_REQUIRED"] = "true"
     server_url = args.server_url
     loop = asyncio.get_event_loop()
     loop.create_task(connect_server(server_url))
@@ -33,10 +31,6 @@ def main():
     
     subparsers = parser.add_subparsers()
 
-    # Init command
-    parser_init = subparsers.add_parser("init")
-    parser_init.set_defaults(func=init)
-
     # Start server command
     parser_start_server = subparsers.add_parser("start-server")
     parser_start_server.add_argument("--host", type=str, default="0.0.0.0")
diff --git a/bioengine/app_loader.py b/bioengine/app_loader.py
new file mode 100644
index 0000000..ccf3a40
--- /dev/null
+++ b/bioengine/app_loader.py
@@ -0,0 +1,45 @@
+from pydantic import BaseModel
+from pathlib import Path
+import logging
+from yaml import safe_load
+from typing import Callable, Optional
+import sys
+import importlib.util
+
+logger = logging.getLogger(__name__)
+
+# define runtime type enum for app runtime
+class AppRuntime(str):
+    python = "python"
+    pyodide = "pyodide"
+    triton = "triton"
+
+class AppInfo(BaseModel):
+    name: str
+    id: str
+    description: str
+    runtime: AppRuntime
+    entrypoint: Optional[str] = None
+    
+    async def run(self, server):
+        if self.runtime == AppRuntime.python:
+            assert self.entrypoint
+                        
+            file_path = Path(__file__).parent.parent / "apps" / self.id / self.entrypoint
+            module_name = 'bioengine.apps.' + self.id.replace('-', '_')
+            spec = importlib.util.spec_from_file_location(module_name, file_path)
+            module = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(module)
+            assert hasattr(module, "hypha_startup")
+            await module.hypha_startup(server)
+
+def load_apps():
+    current_dir = Path(__file__).parent
+    apps_dir = current_dir.parent / "apps"
+    # list folders under apps_dir
+    for app_dir in apps_dir.iterdir():
+        if app_dir.is_dir():
+            manifest_file = app_dir / "manifest.yaml"
+            if manifest_file.exists():
+                manifest = safe_load(manifest_file.read_text())
+                yield AppInfo.parse_obj(manifest)
diff --git a/bioengine/services/__init__.py b/bioengine/services/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/bioengine/services/cellpose/__init__.py b/bioengine/services/cellpose/__init__.py
deleted file mode 100644
index 7970d8a..0000000
--- a/bioengine/services/cellpose/__init__.py
+++ /dev/null
@@ -1,22 +0,0 @@
-
-import tritonclient
-
-async def hypha_startup(server):
-    hypha_launcher = await server.get_service("hypha-launcher")
-    triton_server = await hypha_launcher.launch(image="nvcr.io/nvidia/tritonserver:22.04-py3", command="tritonserver --model-repository=/models", name="triton", ports=[8000])
-    
-    async def train(**kwargs):
-        return tritonclient.execute(**kwargs, server_url=triton_server.server_url)
-
-    await server.register_service({
-        "id": "cellpose",
-        "name": "Cellpose",
-        "description": "A service to run cellpose",
-        "config":{
-            "visibility": "public",
-            "run_in_executor": True,
-        },
-        "train": train,
-    })
-
-print("Hypha startup script loaded")
\ No newline at end of file
diff --git a/bioengine/services/http-file-server/__init__.py b/bioengine/services/http-file-server/__init__.py
deleted file mode 100644
index 0feb5e9..0000000
--- a/bioengine/services/http-file-server/__init__.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import micropip
-await micropip.install(["ssl", "fastapi==0.70.0"])
-
-import random
-import string
-import os
-from fastapi import FastAPI, HTTPException
-from fastapi.responses import FileResponse
-
-def create_fastapi_app(server_url):
-    app = FastAPI()
-    
-    @app.get("/files/{path:path}")
-    async def serve_my_app(path: str):
-        # Construct the full file path
-        file_path = os.path.abspath(os.path.join("/mnt", path))
-        
-        # Security check: Ensure the file path is within /mnt directory
-        if not file_path.startswith(os.path.abspath("/mnt")):
-            raise HTTPException(status_code=400, detail="Invalid file path")
-
-        # Check if the path is a file and serve it
-        if os.path.isfile(file_path):
-            return FileResponse(file_path)
-        else:
-            raise HTTPException(status_code=404, detail="File not found")
-        
-    @app.get("/", response_class=HTMLResponse)
-    async def index():
-        files = os.listdir("/mnt")
-        return f'''
-        <html>
-            <head>
-                <title>Hello</title>
-            </head>
-            <body>
-                <h1>Files</h1>
-                <ul>
-                    {"".join([f'<li><a href="./files/{f}">{f}</a></li>' for f in files])}
-                </ul>
-                <br>
-                <img style="width: 500px" src="https://cataas.com/cat">
-            </body>
-        </html>
-        '''
-    return app
-
-async def hypha_startup(server):
-    # Registering fastapi app
-    connection_info = await server.get_connection_info()
-    fastapi_app = create_fastapi_app(connection_info["public_base_url"])
-    async def serve_fastapi(args):
-        scope = args["scope"]
-        print(f'{scope["client"]} - {scope["method"]} - {scope["path"]}')
-        await fastapi_app(args["scope"], args["receive"], args["send"])
-
-    await server.register_service({
-        "id": "http-" + ''.join(random.choices(string.ascii_uppercase + string.digits, k=5)),
-        "name": "FastAPI HTTP App",
-        "description": "A http server to serve all the mounted files in a simple example page.",
-        "type": "ASGI",
-        "serve": serve_fastapi,
-        "config":{
-            "visibility": "public"
-        },
-        "example_script": f"""print("HTTP server running at {connection_info.public_base_url}/{server.config['workspace']}/apps/fastapi-http-app/")"""
-    })
-    
-    print(f"Server app running at {connection_info.public_base_url}/{server.config['workspace']}/apps/fastapi-http-app/")
-
-print("Hypha startup script loaded")
\ No newline at end of file
diff --git a/environments/pyimagej-py310.yml b/environments/pyimagej-py310.yml
new file mode 100644
index 0000000..40f874a
--- /dev/null
+++ b/environments/pyimagej-py310.yml
@@ -0,0 +1,7 @@
+name: pyimagej-py310
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+ - pyimagej=1.4.1
+ - openjdk=8
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 6a9ba71..dfc52a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,6 +8,9 @@ readme = "README.md"
 description = "Hypha Services for the BioEngine"
 dependencies = [
   "imjoy-rpc",
+  "PyYAML",
+  "hypha-launcher",
+  "pyotritonclient"
 ]
 
 [tool.setuptools]
diff --git a/requirements.txt b/requirements.txt
index 9ac62f2..0da3eee 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,5 @@
 imjoy-rpc
-hypha
\ No newline at end of file
+hypha
+PyYAML==0.6.1
+hypha-launcher
+pyotritonclient
\ No newline at end of file