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tutorial for move_channel_{x,y,z} (#284)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Manually moving channels around\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "\n", | ||
| "With PLR, you can easily move individual channels around. This is useful for calibrating labware locations, calibrating labware sizes, and other things.\n", | ||
| "\n", | ||
| "```{warning}\n", | ||
| "Be very careful about collisions! Move channels to a safe z height before traversing.\n", | ||
| "```\n", | ||
| "\n", | ||
| "```{note}\n", | ||
| "With Hamilton robots, when a tip is mounted, the z location will refer to the point of the pipetting tip. With no tip mounted, it will refer to the bottom of the channel.\n", | ||
| "```" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Example: Hamilton STAR\n", | ||
| "\n", | ||
| "Here, we'll use a Hamilton STAR as an example. For other robots, simply change the deck layout, makign sure that you have at least a tip rack to use." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from pylabrobot.liquid_handling import LiquidHandler, STAR\n", | ||
| "from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, HTF_L\n", | ||
| "\n", | ||
| "lh = LiquidHandler(backend=STAR(), deck=STARDeck())\n", | ||
| "await lh.setup()\n", | ||
| "\n", | ||
| "# assign a tip rack\n", | ||
| "tip_carrier = TIP_CAR_480_A00(name=\"tip_carrier\")\n", | ||
| "tip_carrier[0] = tip_rack = HTF_L(name=\"tip_rack\")\n", | ||
| "lh.deck.assign_child_resource(tip_carrier, rails=0)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Moving channels\n", | ||
| "\n", | ||
| "All positions are in mm. The movements are to absolute positions. The origin will be near the left front bottom of the deck, but it differs between robots.\n", | ||
| "\n", | ||
| "* x: left (low) to right (high)\n", | ||
| "* y: front (low) to back (high)\n", | ||
| "* z: bottom (low) to top (high)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "channel = 1 # the channel to use\n", | ||
| "\n", | ||
| "# start by picking up a single tip\n", | ||
| "await lh.pick_up_tips(tip_rack[\"A1\"], use_channels=[channel])\n", | ||
| "\n", | ||
| "# prepare for manual operation\n", | ||
| "# this will space the other channels to safe positions\n", | ||
| "await lh.prepare_for_manual_channel_operation(channel)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Since the channnel will be above the tip rack, it should be safe to move up. We perform a quick check to make sure the z_safe is at least above the resources we know about." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "z_safe = 240 # WARNING: this might NOT be safe for your setup\n", | ||
| "\n", | ||
| "if z_safe <= lh.deck.get_heighest_known_point():\n", | ||
| " raise ValueError(f\"z_safe position is not safe, it is lower than the highest known point: {lh.deck.get_heighest_known_point()}\")\n", | ||
| "\n", | ||
| "await lh.move_channel_z(channel, z_safe)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "```{warning}\n", | ||
| "The z position in the code above should be safe for most setups, but we can't guarantee that it will be safe for all setups. Move to a z position that is above all your labware before moving in the xy plane.\n", | ||
| "```\n", | ||
| "\n", | ||
| "When the z position of the bottom of the tip is above the labware, you can move the channel around in the xy plane." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# move the channel around\n", | ||
| "await lh.move_channel_x(channel, 100)\n", | ||
| "await lh.move_channel_y(channel, 100)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "After reaching a spot where the channel can move down, you can use `move_channel_z` again." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "await lh.move_channel_z(channel, 100)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Before returning the tip to the tip rack, make sure to move the channel to a safe z position again." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "await lh.move_channel_z(channel, z_safe)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "You can run the code above as often as you like. When you're done, you can return the channel to the tip rack." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "await lh.return_tips()" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "env", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.2" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 2 | ||
| } |
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