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Merge pull request #53 from machineagency/quick_changes
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‎docs/notebooks/Labware_Object_Demo.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "ca4352ca",
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"metadata": {},
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"outputs": [],
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"source": [
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"from labware.Labware import Labware"
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"from science_jubilee.labware.Labware import Labware"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "4a7e9ac8",
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"metadata": {},
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"outputs": [
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"wellPlate: 20mlscintillation_12_wellplate_18000ul"
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]
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},
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "7091aef9",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"Well(name='C3', depth=53, totalLiquidVolume=18000, shape='circular', diameter=27.85, xDimension=None, yDimension=None, x=77.47, y=15.03, z=7.5, offset=None)"
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"Well(name='C3', depth=53, totalLiquidVolume=18000, shape='circular', diameter=27.85, xDimension=None, yDimension=None, x=77.47, y=15.03, z=7.5, offset=None, slot=None)"
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"execution_count": 8,
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"id": "53e3df86",
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{
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"data": {
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"text/plain": [
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"Well(name='C3', depth=53, totalLiquidVolume=18000, shape='circular', diameter=27.85, xDimension=None, yDimension=None, x=77.47, y=15.03, z=7.5, offset=None)"
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"Well(name='B4', depth=53, totalLiquidVolume=18000, shape='circular', diameter=27.85, xDimension=None, yDimension=None, x=105.3, y=42.86, z=7.5, offset=None, slot=None)"
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"outputs": [
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"77.47"
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"metadata": {},
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"53"
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"id": "15e8a5bf",
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"outputs": [
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"60.5"
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]
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},
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"lab[10].top # the actual top of the well"
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"lab[10].top_ # the actual top of the well"
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]
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},
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{
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"cell_type": "markdown",
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"id": "0e23606e",
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"metadata": {},
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"source": [
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"However, you can also indicate a `z` position with resposect to the top or bottom of the well.\n",
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"The `x` and `y` coordinates are the same, this command will change the `z` coordinate and return a Location(Point, Well) object"
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]
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},
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"cell_type": "code",
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"metadata": {},
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"outputs": [
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"data": {
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"text/plain": [
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"7.5"
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"Location(point=(105.3, 42.86, 12.5), labware=Well(name='B4', depth=53, totalLiquidVolume=18000, shape='circular', diameter=27.85, xDimension=None, yDimension=None, x=105.3, y=42.86, z=7.5, offset=None, slot=None))"
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"lab[10].bottom"
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"lab[10].bottom(+5) "
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]
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},
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{
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"outputs": [
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"data": {
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"text/plain": [
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"dict_keys(['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4', 'C1', 'C2', 'C3', 'C4'])"
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"dict_keys(['A1', 'B1', 'C1', 'A2', 'B2', 'C2', 'A3', 'B3', 'C3', 'A4', 'B4', 'C4'])"
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]
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"execution_count": 16,
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"data": {
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"dict_keys(['A1', 'B1', 'C1', 'A2', 'B2', 'C2', 'A3', 'B3', 'C3', 'A4', 'B4', 'C4'])"
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"dict_keys(['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4', 'C1', 'C2', 'C3', 'C4'])"
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"dict_keys(['A1', 'B1', 'C1', 'A2', 'B2', 'C2', 'A3', 'B3', 'C3', 'A4', 'B4', 'C4'])"
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"dict_keys(['A1', 'A2', 'A3', 'A4', 'B1', 'B2', 'B3', 'B4', 'C1', 'C2', 'C3', 'C4'])"
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"output_type": "stream",
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"text": [
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"Well Coordinates for well A1\n",
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"x: 23.81\n",
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"y: 73.69\n",
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"z: 10.95\n"
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"x: 21.81\n",
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"y: 70.69\n",
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"z: 7.5\n"
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},
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"print('Offset : {}'.format(lab[0].offset))"
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{
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"cell_type": "markdown",
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"id": "e53a2ea3",
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"metadata": {},
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"source": [
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"### 5. Manual Labware Offset Calibration\n",
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"\n",
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"There may be instances in which the squaring between the deck and the carriage arm of your Jubilee might not be 100% the same. \n",
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"To avoid issues with your labware positionining, we've implemented another offset calibration method. \n",
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"\n",
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"After placing your labware onto the deck slot, you can follow follow the next few steps to record and apply a namual offset for your labware in *that* slot.\n",
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"For this you will record the **true** `x` and `y` coordinates 3 corner wells of your labware. Generally these will be you top left, top right, and bottom right wells. For examples for a 96-well wellplate, these will be : `A1`, `A12`, and `H12`, respectively. \n",
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"\n",
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"Note: you can perform the next steps using the Camera/WebCamera tool if you want, the procedure is the same. \n",
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"\n",
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"1. Pick up a tool (e.g., an OT2 pipette)\n",
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"2. Navigate to your labware **top_left** well\n",
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"3. Use the Duet GUI to move the pipette to the \"actual\" center of your well if the tool is nto perfectly centered over the well. \n",
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"4. Record your new `x` and `y` coordinates as a tuple.\n",
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"5. Repeat steps 2-4 for the **top_right** and **bottom_right** well\n",
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"\n",
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"After this, you can run the `your_labware.manual_offset()` method. This allows also to save these offsets in the labware `.json` file for future use, as well as later on load them back up without having to re-run this procedure. Note: this will need to be repeated if you laod your labware on a different slot *OR* if you take down and re-build your machine. "
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]
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},
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{
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"cell_type": "code",
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"id": "22d80cc6",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"New manual offset applied to 20mlscintillation_12_wellplate_18000ul\n"
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]
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}
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],
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"source": [
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"lab.slot = 0 # this will be taken care of by the deck.load_labware() method\n",
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"UL = (29.3,78.1)\n",
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"UR = (128.0, 77.9)\n",
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"BR = (128.2, 15.3)\n",
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"\n",
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"lab.manual_offset([UL, UR, BR], save= False)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "73b9891e",
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"metadata": {},
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"source": [
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"You can check if the offset was applied by checking the attribute `manualOffset`."
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]
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},
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"id": "1e32ddd0",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'0': [(29.3, 78.1), (128.0, 77.9), (128.2, 15.3)]}"
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]
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},
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"execution_count": 24,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"lab.manualOffset"
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]
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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.9"
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"version": "3.9.12"
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}
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},
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"nbformat": 4,

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