adding to docs pages

machineagency · Dec 1, 2023 · 0e5c608 · 0e5c608
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diff --git a/docs/pdfs/inoculation_loop_tool_assembly.pdf b/docs/pdfs/inoculation_loop_tool_assembly.pdf
diff --git a/docs/source/building/_static/deck.png b/docs/source/building/_static/deck.png
diff --git a/docs/source/building/_static/duckweed.gif b/docs/source/building/_static/duckweed.gif
diff --git a/docs/source/building/_static/inoculation_loop_tool_assembly.pdf b/docs/source/building/_static/inoculation_loop_tool_assembly.pdf
diff --git a/docs/source/building/_static/pipette-flexure.jpg b/docs/source/building/_static/pipette-flexure.jpg
diff --git a/docs/source/building/building_tools.rst b/docs/source/building/building_tools.rst
@@ -94,6 +94,20 @@ All tools which are supported in ``science_jubilee`` are documented here. For ex
 
             Syringe Tool
 
+    .. card:: Lab Automation Deck
+
+        Deck attachment to hold 6 standard microplates + disposal containers
+
+        +++
+
+        .. button-ref:: lab_automation_deck
+            :ref-type: ref
+            :click-parent:
+            :color: secondary
+            :expand:
+
+            Lab Automation Deck
+
 .. card:: Tool Postrequisites
     :class-card: intro-card
     :shadow: md

diff --git a/docs/source/building/inoculation_tool.rst b/docs/source/building/inoculation_tool.rst
@@ -17,7 +17,12 @@ The inoculation loop tool uses the existing `pen tool <https://jubilee3d.com/ind
 Parts to Buy
 ============
 * Inoculation loop
+* See the `Jubilee pen tool <https://jubilee3d.com/index.php?title=Passive_Pen_Tool>`_ for all fabrication other files
 
 Parts to 3D Print
 =================
 * Beyond the pen tool parts documented at the Jubilee project page, we have a customizable inoculation loop `design <https://www.thingiverse.com/thing:5523037>`_ to move heavy duckweed fronds. 
+
+Assembly
+========
+Find step-by-step build instructions `here <https://github.com/machineagency/science_jubilee/tree/main/docs/pdfs/inoculation_loop_tool_assembly.pdf>`_
diff --git a/docs/source/building/lab_automation_deck.rst b/docs/source/building/lab_automation_deck.rst
@@ -0,0 +1,27 @@
+.. _lab_automation_deck:
+
+*******************
+Lab Automation Deck
+*******************
+
+.. figure:: _static/deck.png
+    :scale: 50 %
+    :alt: deck
+
+    A lab automation deck with a variety of labware installed.
+
+Last Edited: Blair, 2023.11.30
+
+There is also a lab automation deck documented `on the Jubilee Wiki <https://jubilee3d.com/index.php?title=Lab_Automation_Plate>`_. The deck attachment here is easier to build, requires less materials, and has slots off the build plate for disposal (e.g. sharps) containers. It also uses a flexure based design to accommodate slight labware heterogeneity. If you are working with more dangerous or expensive materials, the attachment on the Jubilee Wiki can provide greater stability. 
+
+Parts to Buy
+============
+*  `1/8" Delrin <https://www.onlinemetals.com/en/buy/plastic/0-125-acetal-sheet-homopolymer-delrin-natural/pid/6761>`_
+
+Parts to Fabricate
+==================
+* Design files for the deck can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/bed_plate/fabrication_files>`_
+
+Duet Config Files
+=================
+* The Jubilee homing routine needs to be adjusted to probe points on the platform, rather than the deck attachment. Find the udpated config files here `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/bed_plate/duet_config>`_
diff --git a/docs/source/building/pipette_tool.rst b/docs/source/building/pipette_tool.rst
@@ -6,7 +6,7 @@ Pipette Tool
 
 Last Edited: Blair, 2023.11.11
 
-.. figure:: _static/pipette.jpg
+.. figure:: _static/pipette-flexure.jpg
     :scale: 50 %
     :alt: Front and back of the pipette tool.
 
@@ -21,10 +21,11 @@ Last Edited: Blair, 2023.11.11
 Parts to Buy
 ============
 * OT-2 Pipette (tested with gen1 and gen2)
+* See the shopping list for tool parts `here <https://docs.google.com/spreadsheets/d/1Bp4ZdpHsX01EHIsc5mqbzi92CpQlax4KNS-QtPmUZUM/edit#gid=1582949094>`_
 
 Parts to Fabricate
 ==================
-* Pipette tool frame and correctly sized parking posts can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/OT2_pipette/fabrication_files>`_
+* Pipette tool frame SolidWorks file and correctly sized parking posts can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/OT2_pipette/fabrication_files>`_
 
 Electronics
 ===========

diff --git a/docs/source/building/side_camera_tool.rst b/docs/source/building/side_camera_tool.rst
@@ -14,10 +14,12 @@ Last Edited: Blair, 2023.11.11
 
 Parts to Buy
 ============
-* `Adjustable Focus USB Camera <https://www.amazon.com/gp/product/B07YHJK4LN/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&th=1>`_
-* `USB Extension Cable <https://www.amazon.com/dp/B00NH11PEY>`_
+* The frame is compatible with this `Adjustable Focus USB Camera <https://www.amazon.com/gp/product/B07YHJK4LN/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&th=1>`_
+* We use a `USB Extension Cable <https://www.amazon.com/dp/B00NH11PEY>`_ to connect to the Raspberry Pi
+* All other parts can be found in the shopping list `here <https://docs.google.com/spreadsheets/d/1GQ_mkORPUlO9c32SF99uSSLCm2VZMwjv7bX0434kW1c/edit#gid=1582949094>`_
 
 
 Parts to 3D Print
 =================
-* All parts to print can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/camera_side/STLs>`_
+* All parts to print can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/camera_side/STLs>`_
+* The SolidWorks files can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/camera_side/CADs>`_
diff --git a/docs/source/building/syringe_tool.rst b/docs/source/building/syringe_tool.rst
@@ -17,7 +17,9 @@ See the `10cc Syringe tool <https://jubilee3d.com/index.php?title=Camera_Inspect
 Parts to Buy
 ============
 * Syringe (10cc or 50cc)
+* The full shopping list can be found `here <https://docs.google.com/spreadsheets/d/19zSPgaUJId5xt-jpjvXQGE22AiIK3zP_XUoAT0gs4UI/edit#gid=1582949094>`_ and is the same for both the 10cc and 50cc syringe.
 
 Parts to 3D Print
 =================
-* Files for a 50cc syringe can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/syringe_50cc/STLs>`_. See above for 10cc syringe.
+* Parts to print for a 50cc syringe can be found `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/syringe_50cc/STLs>`_. See above for 10cc syringe.
+* SolidWork files for the 50cc syringe parts are `here <https://github.com/machineagency/science_jubilee/tree/main/tool_library/syringe_50cc/cads>`_
diff --git a/docs/source/building/top_down_camera_tool.rst b/docs/source/building/top_down_camera_tool.rst
@@ -4,6 +4,12 @@
 Camera Tool
 ***********
 
-Last Edited: Blair, 2023.11.10
+Last Edited: Blair, 2023.11.30
 
-See the `Camera Inspection Tool <https://jubilee3d.com/index.php?title=Camera_Inspection_Tool>`_ documented on the Jubilee project page.
+.. figure:: _static/duckweed.gif
+    :scale: 25 %
+    :alt: Timelapse of duckweed growing.
+
+    A timelapse of duckweed frond growth, taken with the Jubilee camera tool.
+
+See the `Camera Inspection Tool <https://jubilee3d.com/index.php?title=Camera_Inspection_Tool>`_ documented on the Jubilee project page for all fabrication files and a shopping list.
diff --git a/docs/source/getting_started/deck_guide.rst b/docs/source/getting_started/deck_guide.rst
@@ -26,7 +26,7 @@ The standard lab automation deck consists of 6 slots (indices 0-5), and a number
     Orientation of slots on deck and labware in slots.
 
 
-To use the lab automation deck, we need to set the offsets for each of the 6 slots, as well as any off-deck containers, and place the definition in the ``decks/deck_definitions/`` directory. The preferred method to do so accurately is with a camera tool; the `deck definition calibration notebook <>`_ interactively guides you through this process. If you do not have a camera tool, this can also be done using any other tool that extends into the build volume such that you can accurately align the tool tip to the top-right corner of each slot.
+To use the lab automation deck, we need to set the offsets for each of the 6 slots, as well as any off-deck containers, and place the definition in the ``decks/deck_definitions/`` directory. The preferred method to do so accurately is with a camera tool; the `deck definition calibration notebook <https://github.com/machineagency/science_jubilee/blob/main/science_jubilee/calibration/LabAutomationDeckCalibration.ipynb>`_ interactively guides you through this process. If you do not have a camera tool, this can also be done using any other tool that extends into the build volume such that you can accurately align the tool tip to a corner of each slot.
 
 Creating Labware Definitions
 ============================
@@ -49,7 +49,25 @@ We can then load a deck onto the machine, and labware into the deck::
   m = Machine()
   deck = m.load_deck("<my_deck_definition>")
   labware = deck.load_labware("<my_labware_defintion>")
+
+
+Note that we can omit the ``.json`` file extension. Let's take an example using a 24-well plate. Each labware is made up of a numbe of ``Well`` objects. We can access information like size and location of each well by its row-column identification (A1, A2, ...) or its index (0, 1, ...), where index 0 corresponds to A1:: 
+
+  labware = deck.load_labware("greiner_24_wellplate_3300ul", 1)
+  well = labware["A1"] # Identical to labware[0]
+
+The value of ``well`` for this labware is:: 
+
+  Well(name='A1', depth=16.5, totalLiquidVolume=3300, shape='circular', 
+      diameter=16.28, xDimension=None, yDimension=None, x=175.13, 
+      y=79.3, z=2.5, offset=[160.0, 7.3])
+
+The value of ``offset`` comes from your specific automation deck calibration, and is used to adjust the position of each well. All other information derives from your labware definition. We can access each attribute directly:: 
+
+  well.x      # 175.13, the x position of the well center
+  well.y      # 79.3,   the y position of the well center
+  well.depth  # 16.5,   the usable depth of this well from the top of the labware
+  well.z      # 7.5,    the thickness of the labware plate
+
 
-Note that we can omit the ``.json`` file extension. 
 
-*in progress*
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -80,7 +80,7 @@ Welcome to the Science Jubilee docs! This website contains information for lab a
 What is a Science Jubilee?
 --------------------------
 
-`Jubilee <https://jubilee3d.com/index.php?title=Main_Page>`_ is an open-source & extensible multi-tool motion platform. If that doesn't mean much to you, you can think of it as a 3D printer that can change its tools. ``science_jubilee`` provides tools and associated control software to use Jubilee for laboratory automation. This website contains documentation for various lab automation applications including liquid handling, imaging, and sample manipulation. While these applications might cater exactly to your planned use case, they most likely will not! ``science_jubilee`` is meant to be flexible; hopefully, the examples here provide a foundation for you to design all sorts of niche experiments!
+`Jubilee <https://jubilee3d.com/index.php?title=Main_Page>`_ is an open-source & extensible multi-tool motion platform. If that doesn't mean much to you, you can think of it as a 3D printer that can change its tools. ``science_jubilee`` provides tools and associated control software to use Jubilee for laboratory automation. This website contains documentation for various lab automation applications including liquid handling, imaging, and sample manipulation. While these applications might cater exactly to your planned use case, they most likely will not! ``science_jubilee`` is meant to be flexible; hopefully, the examples here provide a foundation for you to design all sorts of niche experiments.
 
 |pipetting| |duckweed|
 
@@ -91,6 +91,13 @@ What is a Science Jubilee?
    :width: 49%
 
 
+Jubilee is used in various scientific contexts. A few examples include:
+
+* `The Duckbot <https://github.com/machineagency/duckbot>`_, for automating duckweed experiments
+* `Sonication Station <https://github.com/machineagency/sonication_station/>`_, for sonicating samples
+* `Jubiris <https://github.com/bunnie/jubiris/tree/main>`_, for Infra-Red, In-Situ (IRIS) inspection of silicon
+
+We hope that ``science_jubilee`` helps you add to this list-- if you're using Jubilee for lab automation, reach out to be added here!