pycromanager.ipynb

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   "source": [
    "## Setup\n",
    "\n",
    "Before start this notebook, you need to:\n",
    "1. Install ImJoy Jupyter Extension by run `pip install imjoy-jupyter-extension`, restart Jupyter notebook, and make sure you see an ImJoy icon in the toolbar in opened notebooks.\n",
    "1. Download the lastest version of [micro-manager 2.0](https://micro-manager.org/wiki/Micro-Manager_Nightly_Builds)\n",
    "1. Install pycro-manager using `pip install pycromanager`\n",
    "1. Run Micro-Manager, select tools-options, and check the box that says Run server on port 4827 (you only need to do this once)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting pycromanager\n",
      "  Downloading pycromanager-0.4.0-py3-none-any.whl (33 kB)\n",
      "Requirement already satisfied, skipping upgrade: zmq in ./miniconda3/lib/python3.7/site-packages (from pycromanager) (0.0.0)\n",
      "Requirement already satisfied, skipping upgrade: dask[array]>=2.4.0 in ./miniconda3/lib/python3.7/site-packages (from pycromanager) (2.10.1)\n",
      "Requirement already satisfied, skipping upgrade: numpy in ./miniconda3/lib/python3.7/site-packages (from pycromanager) (1.19.1)\n",
      "Requirement already satisfied, skipping upgrade: pyzmq in ./miniconda3/lib/python3.7/site-packages (from zmq->pycromanager) (18.0.2)\n",
      "Requirement already satisfied, skipping upgrade: toolz>=0.7.3; extra == \"array\" in ./miniconda3/lib/python3.7/site-packages (from dask[array]>=2.4.0->pycromanager) (0.10.0)\n",
      "Installing collected packages: pycromanager\n",
      "  Attempting uninstall: pycromanager\n",
      "    Found existing installation: pycromanager 0.2.5\n",
      "    Uninstalling pycromanager-0.2.5:\n",
      "      Successfully uninstalled pycromanager-0.2.5\n",
      "Successfully installed pycromanager-0.4.0\n"
     ]
    }
   ],
   "source": [
    "!pip install -U pycromanager"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "window.connectPlugin && window.connectPlugin()"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div id=\"42ccc43b-b43e-4b57-be9a-6b49ee1e0497\"></div>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import numpy as np\n",
    "from imjoy_rpc import api\n",
    "from pycromanager import Bridge\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        bridge = Bridge()\n",
    "        self._core = bridge.get_core()\n",
    "        self._core.set_exposure(float(100))\n",
    "        exposure = self._core.get_exposure()\n",
    "        api.showMessage('MMcore loaded, exposure: ' + str(exposure))\n",
    "    \n",
    "    def snapImage(self):\n",
    "        self._core.snap_image()\n",
    "        tagged_image = self._core.get_tagged_image()\n",
    "        image_array = np.reshape(tagged_image.pix, newshape=[tagged_image.tags['Height'], tagged_image.tags['Width']])\n",
    "        image_array = (image_array/image_array.max()*255).astype('uint8')\n",
    "        return image_array\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        viewer = await api.showDialog(type=\"itk-vtk-viewer\",\n",
    "                                      src=\"https://oeway.github.io/itk-vtk-viewer/?imjoy=1\")\n",
    "        api.showMessage('Acquiring 10 images')\n",
    "        for i in range(10):\n",
    "            await viewer.imshow(self.snapImage())\n",
    "        api.showMessage('Done.')\n",
    "        \n",
    "api.export(ImJoyPlugin(), {\"name\": \"demo\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/javascript": [
       "window.connectPlugin && window.connectPlugin()"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div id=\"b7fd70f9-fb0c-4dfb-8b38-55247dc6929e\"></div>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import asyncio\n",
    "import numpy as np\n",
    "\n",
    "class ImJoyPlugin():\n",
    "    async def setup(self):\n",
    "        bridge = Bridge()\n",
    "        self._core = bridge.get_core()\n",
    "        self._core.set_exposure(float(100))\n",
    "        exposure = self._core.get_exposure()\n",
    "        api.showMessage('MMcore loaded, exposure: ' + str(exposure))\n",
    "    \n",
    "    def snapImage(self):\n",
    "        self._core.snap_image()\n",
    "        tagged_image = self._core.get_tagged_image()\n",
    "        image_array = np.reshape(tagged_image.pix, newshape=[tagged_image.tags['Height'], tagged_image.tags['Width']])\n",
    "        image_array = (image_array/image_array.max()*255).astype('uint8')\n",
    "        return image_array\n",
    "\n",
    "    async def run(self, ctx):\n",
    "        viewer = await api.createWindow(src=\"https://kaibu.org/#/app\")\n",
    "\n",
    "        image = np.random.randint(0, 255, [500, 500], dtype='uint8')\n",
    "\n",
    "        # view image\n",
    "        await viewer.view_image(self.snapImage(), type=\"itk-vtk\", name=\"new image\")\n",
    "\n",
    "        async def snap_image():\n",
    "            await viewer.view_image(self.snapImage(), type=\"itk-vtk\", name=\"new image\")\n",
    "\n",
    "        await viewer.set_ui({\"title\": \"Microscope Control\",\n",
    "                             \"elements\": [\n",
    "                                 {\"_rintf\": True,\n",
    "                                  \"type\": \"button\",\n",
    "                                  \"label\": \"Snap Image\",\n",
    "                                  \"callback\": snap_image\n",
    "                                 }\n",
    "                             ]\n",
    "                            })\n",
    "\n",
    "api.export(ImJoyPlugin(), {\"name\": \"demo\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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PycroManagerTest-Kaibu.py

import asyncio
import numpy as np

class ImJoyPlugin():
    async def setup(self):
        bridge = Bridge()
        self._core = bridge.get_core()
        self._core.set_exposure(float(100))
        exposure = self._core.get_exposure()
        api.showMessage('MMcore loaded, exposure: ' + str(exposure))
    
    def snapImage(self):
        self._core.snap_image()
        tagged_image = self._core.get_tagged_image()
        image_array = np.reshape(tagged_image.pix, newshape=[tagged_image.tags['Height'], tagged_image.tags['Width']])
        image_array = (image_array/image_array.max()*255).astype('uint8')
        return image_array

    async def run(self, ctx):
        viewer = await api.createWindow(src="https://kaibu.org/#/app")

        image = np.random.randint(0, 255, [500, 500], dtype='uint8')

        # view image
        await viewer.view_image(self.snapImage(), type="itk-vtk", name="new image")

        async def snap_image():
            await viewer.view_image(self.snapImage(), type="itk-vtk", name="new image")

        await viewer.set_ui({"title": "Microscope Control",
                             "elements": [
                                 {"_rintf": True,
                                  "type": "button",
                                  "label": "Snap Image",
                                  "callback": snap_image
                                 }
                             ]
                            })

api.export(ImJoyPlugin(), {"name": "demo"})

PycroManagerTest.py

import numpy as np
from imjoy_rpc import api
from pycromanager import Bridge

class ImJoyPlugin():
    async def setup(self):
        bridge = Bridge()
        self._core = bridge.get_core()
        exp = await api.prompt('Exposure time')
        self._core.set_exposure(float(exp))
        exposure = self._core.get_exposure()
        api.showMessage('MMcore loaded, exposure: ' + str(exposure))
    
    def snapImage(self):
        self._core.snap_image()
        tagged_image = self._core.get_tagged_image()
        image_array = np.reshape(tagged_image.pix, newshape=[tagged_image.tags['Height'], tagged_image.tags['Width']])
        image_array = (image_array/image_array.max()*255).astype('uint8')
        return image_array

    async def run(self, ctx):
        viewer = await api.showDialog(type="itk-vtk-viewer",
                                      src="https://oeway.github.io/itk-vtk-viewer/?imjoy=1")
        api.showMessage('Acquiring 10 images')
        for i in range(10):
            await viewer.imshow(self.snapImage())
        api.showMessage('Done.')
        
api.export(ImJoyPlugin(), {"name": "demo"})