diff --git a/make.bat b/make.bat deleted file mode 100644 index 8b116ef..0000000 --- a/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=docs - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/source/conf.py b/source/conf.py index 1a716c5..ccb1c12 100644 --- a/source/conf.py +++ b/source/conf.py @@ -232,8 +232,13 @@ } # Option for linkcheck -linkcheck_anchors = False +linkcheck_anchors = True + +linkcheck_anchors_ignore = [ + 'imaging-your-surroundings', + 'glueepoxy' +] suppress_warnings = [ - 'image.not_readable' + # 'image.not_readable' ] \ No newline at end of file diff --git a/source/overview/accessories.rst b/source/overview/accessories.rst index 383ef1a..988486d 100644 --- a/source/overview/accessories.rst +++ b/source/overview/accessories.rst @@ -12,18 +12,18 @@ There are accessories that are frequently used with miniscopes. Those include: ***************************** Open Ephys Coaxial Commutator ***************************** - -.. image:: commutator-ucla-miniscope-v4-ophelia.webp - :alt: animated image of the commutator rotating the tether when ophelia is rotated +.. + .. image:: commutator-ucla-miniscope-v4-ophelia.webp + :alt: animated image of the commutator rotating the tether when ophelia is rotated The Open Ephys Coaxial Commutator (`documentation `_, `store `_, `github `_) enables twist-free connection between a stationary data acquisition device and the UCLA Miniscope v4 mounted onto a freely-moving animal. This promotes natural animal behavior by nearly eliminating mechanical stress during neurophysiology experiments. This also improves signal reliability by maintaining electrical continuity between stationary and moving electronics. It accomplishes this by utilizing the IMU on-board the UCLA Miniscope v4 PCB to sense the orientation of the miniscope and rotate the tether accordingly. For a guide to using the UCLA Miniscope v4 using the commutator, please refer to these guides: `Automating Commutation with ONIX and UCLA Miniscope v4 `_ or `Automating Commutation with Miniscope DAQ and UCLA Miniscope v4 `_. ************ UCLA MiniCam ************ - -.. image:: ucla-miniscope-v4_minicam-data.webp - :alt: image of minicam & minicam data +.. + .. image:: ucla-miniscope-v4_minicam-data.webp + :alt: image of minicam & minicam data .. todo:: fix refs. gitref? diff --git a/source/overview/miniscopes.rst b/source/overview/miniscopes.rst index 2c4d338..c13484d 100644 --- a/source/overview/miniscopes.rst +++ b/source/overview/miniscopes.rst @@ -8,22 +8,23 @@ To understand broadly what a miniscope is, refer to the :ref:`overview/index:Wha Open Ephys sells the following miniscopes: .. todo:: replace with image of ONIX 2.0 once that exists - -.. grid:: 2 - - .. grid-item-card:: UCLA Miniscope v3 Wireless - :link: /ucla-miniscope-v3-wireless/index - :link-type: doc - :link-alt: UCLA Miniscope v3 Wireless index - :img-top: /_static/images/ucla-miniscope-v3-wireless.webp - :img-alt: image of UCLA Miniscope v3 Wireless - - .. grid-item-card:: UCLA Miniscope v4 - :link: /ucla-miniscope-v4/index - :link-type: doc - :link-alt: UCLA Miniscope v4 index - :img-top: /_static/images/ucla-miniscope-v4.webp - :img-alt: image of UCLA Miniscope v4 + +.. + .. grid:: 2 + .. + .. grid-item-card:: UCLA Miniscope v3 Wireless + :link: /ucla-miniscope-v3-wireless/index + :link-type: doc + :link-alt: UCLA Miniscope v3 Wireless index + :img-top: /_static/images/ucla-miniscope-v3-wireless.webp + :img-alt: image of UCLA Miniscope v3 Wireless + + .. grid-item-card:: UCLA Miniscope v4 + :link: /ucla-miniscope-v4/index + :link-type: doc + :link-alt: UCLA Miniscope v4 index + :img-top: /_static/images/ucla-miniscope-v4.webp + :img-alt: image of UCLA Miniscope v4 **************** Comparison Chart diff --git a/source/ucla-miniscope-v4/faq-troubleshoot/faq.rst b/source/ucla-miniscope-v4/faq-troubleshoot/faq.rst index 4b743f2..856a12b 100644 --- a/source/ucla-miniscope-v4/faq-troubleshoot/faq.rst +++ b/source/ucla-miniscope-v4/faq-troubleshoot/faq.rst @@ -131,5 +131,6 @@ Refer to :doc:`/ucla-miniscope-v4/developer/common-mods/lenses-combo` page of th How Do I Adjust Dynamic Range of LED Excitation Light Source? ************************************************************* -Refer to :doc:`/ucla-miniscope-v4/developer/common-mods/led-resistor` page of this documentation. +.. + Refer to :doc:`/ucla-miniscope-v4/developer/common-mods/led-resistor` page of this documentation. diff --git a/source/ucla-miniscope-v4/faq-troubleshoot/troubleshoot.rst b/source/ucla-miniscope-v4/faq-troubleshoot/troubleshoot.rst index f9bfc80..545ef31 100644 --- a/source/ucla-miniscope-v4/faq-troubleshoot/troubleshoot.rst +++ b/source/ucla-miniscope-v4/faq-troubleshoot/troubleshoot.rst @@ -6,9 +6,9 @@ Troubleshooting ******************************* Image Contains Stripes or Bands ******************************* - -.. image:: horizontal-stripes.webp - :alt: image of black horizontal stripes on UCLA Miniscope v4 mimage +.. + .. image:: horizontal-stripes.webp + :alt: image of black horizontal stripes on UCLA Miniscope v4 mimage The stripes appear when there is a bad connection between the Miniscope and the DAQ, so there is a mismatch between frames coming to the DAQ. Would you check if the coaxial cable has any signs of wear or damage? diff --git a/source/ucla-miniscope-v4/quick-start/index.rst b/source/ucla-miniscope-v4/quick-start/index.rst index d5c3a47..6204a1c 100644 --- a/source/ucla-miniscope-v4/quick-start/index.rst +++ b/source/ucla-miniscope-v4/quick-start/index.rst @@ -5,8 +5,9 @@ Quick Start Guide .. todo:: create the below image of miniscope responding to adjustment of LED intensity and imaging depth -.. image:: /_static/images/ucla-miniscope-v4-in-action.webp - :alt: image of ucla miniscope v4 in action +.. + .. image:: /_static/images/ucla-miniscope-v4-in-action.webp + :alt: image of ucla miniscope v4 in action The `Quick Start Guide` serves to familiarize yourself with and validate the functionaliy of the UCLA Miniscope v4 and associated hardware. For acquiring and analyzing data, refer to the :doc:`/ucla-miniscope-v4/user/index`. diff --git a/source/ucla-miniscope-v4/quick-start/miniscope-daq-quick.rst b/source/ucla-miniscope-v4/quick-start/miniscope-daq-quick.rst index dba00bb..528de09 100644 --- a/source/ucla-miniscope-v4/quick-start/miniscope-daq-quick.rst +++ b/source/ucla-miniscope-v4/quick-start/miniscope-daq-quick.rst @@ -23,33 +23,39 @@ Connect Hardware * Connect Miniscope-DAQ to the UCLA Miniscope v4 using the provided coaxial SMA plug ↔ MMCX plug tether: - .. image:: /_static/images/sma-plug_mmcx-plug_cable.webp - :alt: photograph of provided coaxial SMA plug ↔ MMCX plug cable + .. .. image:: /_static/images/sma-plug_mmcx-plug_cable.webp - * Insert the cable’s SMA plug into Miniscope-DAQ’s SMA jack labeled `Miniscope`. Gently hand-tighten the SMA connector with light-force until you are no longer able to turn the connector + .. :alt: photograph of provided coaxial SMA plug ↔ MMCX plug cable - .. image:: /_static/images/cable-sma-plug_miniscope-daq-sma-jack.webp - :alt: photograph of sma plug going into miniscope-daq sma jack + * Insert the cable's SMA plug into Miniscope-DAQ's SMA jack labeled `Miniscope`. Gently hand-tighten the SMA connector with light-force until you are no longer able to turn the connector - * Insert the cable’s MMCX plug into UCLA Miniscope’s MMCX jack. Confirm that a click is felt and heard before proceeding from this step. + .. .. image:: /_static/images/cable-sma-plug_miniscope-daq-sma-jack.webp - .. image:: /_static/images/cable-mmcx-plug_ucla-miniscope-v4-mmcx-jack.webp - :alt: photograph of mmcx plug going into ucla miniscope v4 mmcx jack + .. :alt: photograph of sma plug going into miniscope-daq sma jack + + * Insert the cable's MMCX plug into UCLA Miniscope's MMCX jack. Confirm that a click is felt and heard before proceeding from this step. + + .. .. image:: /_static/images/cable-mmcx-plug_ucla-miniscope-v4-mmcx-jack.webp + + .. :alt: photograph of mmcx plug going into ucla miniscope v4 mmcx jack * Connect Miniscope-DAQ to your computer using the provided USB3.0 Micro Type B plug ↔ USB3.0 Type A plug cable: - .. image:: /_static/images/usb3,0-microb-plug_usb3,0-a-plug_cable.webp - :alt: photograph of provided USB3.0 Micro Type B plug ↔ USB3.0 Type A plug cable + .. .. image:: /_static/images/usb3,0-microb-plug_usb3,0-a-plug_cable.webp + + .. :alt: photograph of provided USB3.0 Micro Type B plug ↔ USB3.0 Type A plug cable - * Insert the cable’s USB3.0 Micro Type B plug into the Miniscope-DAQ’s USB3.0 Micro Type B jack located on the Miniscope DAQ’s back face. + * Insert the cable's USB3.0 Micro Type B plug into the Miniscope-DAQ's USB3.0 Micro Type B jack located on the Miniscope DAQ's back face. - .. image:: /_static/images/cable-usb3,0-microb-plug_miniscope-daq-usb3,0-microb-jack.webp - :alt: photograph of usbplug going into miniscope-daq jack + .. .. image:: /_static/images/cable-usb3,0-microb-plug_miniscope-daq-usb3,0-microb-jack.webp + + .. :alt: photograph of usbplug going into miniscope-daq jack - * Insert the cable’s USB3.0 Type A plug into your computer's USB3.0 Type A jack. + * Insert the cable's USB3.0 Type A plug into your computer's USB3.0 Type A jack. - .. image:: /_static/images/cable-usb3,0-a-plug_computer-usb3,0-a-jack.webp - :alt: photograph of usb plug going into computer usb jack + .. .. image:: /_static/images/cable-usb3,0-a-plug_computer-usb3,0-a-jack.webp + + .. :alt: photograph of usb plug going into computer usb jack #. Confirm that all three indicators on the miniscope DAQ are illuminated before proceeding from this step as indicated in the below potos. If not all three indicators are illuminated, refer to :doc:`/ucla-miniscope-v4/faq-troubleshoot/index` section. diff --git a/source/ucla-miniscope-v4/user/analysis/index.rst b/source/ucla-miniscope-v4/user/analysis/index.rst index 8fd4297..4b2c307 100644 --- a/source/ucla-miniscope-v4/user/analysis/index.rst +++ b/source/ucla-miniscope-v4/user/analysis/index.rst @@ -13,5 +13,5 @@ Calcium Imaging Analysis .. toctree:: :hidden: - caiman-pipeline +.. caiman-pipeline diff --git a/source/ucla-miniscope-v4/user/assembly/emission.rst b/source/ucla-miniscope-v4/user/assembly/emission.rst index 3e906e0..0987a1c 100644 --- a/source/ucla-miniscope-v4/user/assembly/emission.rst +++ b/source/ucla-miniscope-v4/user/assembly/emission.rst @@ -12,12 +12,14 @@ Preparation #. Screw the self-tapping screw into the hole in the emission module's side, and unscrew it. Performing this step early serves to provide accessibility to any burrs potentially introduced in the tapping process. It is easier to remove the burrs now than later in the emission module assembly process. If the self-tapping screw does not insert into the hole when initiating the screwing process, slightly open the hole gently with a scalpel. CAREFUL TO NOT PROTRUDE INTO IT. -.. image:: self-tapping.webp +.. + .. image:: self-tapping.webp :alt: image of self-tapping screw being inserted and removed, potentially also opening up hole with scalpel at the start #. Inspect for burrs. If there are burrs, remove them. If they are not loose, use forceps or brush to remove them. If they are loose, blow with compressed air or gently tap the emission module against the work surface such that they fall out. Confirm that there are no burrs before proceeding. Such burrs interfere image formation and are more difficult to remove after the following steps are carried out -.. image:: burr-inspection&removal-emission-1.webp +.. + .. image:: burr-inspection&removal-emission-1.webp :alt: image of inspecting for burrs and removing them **************** @@ -29,17 +31,20 @@ Insert Tube Lens #. Position tube lens convex-down on lens tissue paper on work surface. Confirm the lens wobbles when laterally perturbed. Concentrically align the emission module's bore with the optical axis of the tube lens. -.. image:: tube-lens-wobble.webp +.. + .. image:: tube-lens-wobble.webp :alt: image of tube lens perturbed and wobbling #. Press emission module down and over tube lens until emission lens is flush with work surface. Gentle force is acceptable provided that the lens and emission module maintain parallel alignment through the pressing process -.. image:: emission-module-flush.webp +.. + .. image:: emission-module-flush.webp :alt: image of emission module going over tube lens #. Turn the emission module such that the inserted lens is facing up. Press on lens from the bottom using cloth or cotton swab so that the lens is flush with the emission module -.. image:: tube-lens-final-push.webp +.. + .. image:: tube-lens-final-push.webp :alt: image of tube lens being inserted into position ********************** @@ -51,17 +56,20 @@ Insert Dichroic Mirror #. Correctly orient the dichroic mirror on lens tissue paper on work surface. You should be able to see the dichroic mirror's edge through its visible surface. Confirm this is true. This is the surface upon which incoming light is incident. If there is an arrow along the edge of the dichroic mirror, confirm the arrow points down -.. image:: dichroic-mirror-orientation.webp +.. + .. image:: dichroic-mirror-orientation.webp :alt: image of dichroic mirror on work surface correctly oriented #. With the less dominant hand, tilt the emission module such that the lens is facing the work surface and the diagonal slot which the dichroic mirror is supposed to be inserted is facing up. With the more dominant hand and forceps, insert the dichroic mirror into the diagonal slot of the emission module -.. image:: dichroic-mirror-insertion.webp +.. + .. image:: dichroic-mirror-insertion.webp :alt: image of tube lens being inserted into position #. Inspect for burrs or visible debris in the emission module. If there is any, remove it similar to removing burrs before except now you can't use a brush or compressed air because that risks damaging the optics (compressed air sold specifically sold for optics this such as `CA4-US from THORLABS `_ is acceptable, but be careful to blow it aimed at free air before blowing it aimed at optics) -.. image:: burr-inspection&removal-emission-2.webp +.. + .. image:: burr-inspection&removal-emission-2.webp :alt: image of inspecting for burrs and removing them ************************************************** @@ -70,10 +78,12 @@ Insert Half-Ball Lens and Attach Excitation Module #. With the less dominant hand, tilt the emission module such that the lens is facing the work surface and the cavity which the half-ball lens is supposed to be inserted is facing up. With the more dominant hand and forceps, insert the half-ball lens into the into the cavity. The spherical part of the lens should smoothly nest into the cavity -.. image:: halfball-lens-insertion.webp +.. + .. image:: halfball-lens-insertion.webp :alt: image of halfball lens being inserted into position #. Place the excitation module over the half-ball lens. Slowly fasten the excitation module with two screws to secure the half-ball lens and excitation module onto the emission module -.. image:: excitation-module-attachment-to-emission-module.webp +.. + .. image:: excitation-module-attachment-to-emission-module.webp :alt: image of excitation module being fastened into emission module \ No newline at end of file diff --git a/source/ucla-miniscope-v4/user/assembly/excitation.rst b/source/ucla-miniscope-v4/user/assembly/excitation.rst index c014636..385ca16 100644 --- a/source/ucla-miniscope-v4/user/assembly/excitation.rst +++ b/source/ucla-miniscope-v4/user/assembly/excitation.rst @@ -8,15 +8,18 @@ Excitation Module #. Correctly orient filter on lens tissue paper on work surface. You should be able to see the filter's edge through its visible surface. Confirm this is true. This is the surface upon which incoming light is incident. If there is an arrow along the edge of the filter, confirm the arrow points down before proceeding +.. .. image:: filter-orientation.webp :alt: image of filter oriented on work surface: good example and bad example #. Position the excitation module upright such that the filter can be inserted. Place the filter onto the excitation module where it is supposed to be inserted. Maintain the filter's orientation during this process. If the orientation is lost, return to the previous step before proceeding +.. .. image:: filter-excitation-module-inprogress.webp :alt: image of filter oriented in excitation module #. Insert the filter into the excitation module by pressing on it with cotton swabs +.. .. image:: filter-excitation-module-inprogress.webp :alt: image of filter set into its final position in excitation module diff --git a/source/ucla-miniscope-v4/user/assembly/index.rst b/source/ucla-miniscope-v4/user/assembly/index.rst index 71812d1..e2bcb54 100644 --- a/source/ucla-miniscope-v4/user/assembly/index.rst +++ b/source/ucla-miniscope-v4/user/assembly/index.rst @@ -54,12 +54,13 @@ To contextualize the assembly process, a breakdown of each module is provided. F .. tab-item:: PCB - .. image:: /_static/images/pcb-module.webp - :alt: image of pcb module - :align: center - Mounts the various electronics for controlling the sensor, ETL, LED and communication with the data acquisition hardware + .. + .. image:: /_static/images/pcb-module.webp + :alt: image of pcb module + :align: center + The following assembly instructions are divided into distinct steps according to the UCLA Miniscope v4's four modules in addition to a :doc:`/ucla-miniscope-v4/user/assembly/preparation` step and a :doc:`/ucla-miniscope-v4/user/assembly/validate-finish` step. .. todo:: diff --git a/source/ucla-miniscope-v4/user/assembly/objective.rst b/source/ucla-miniscope-v4/user/assembly/objective.rst index d16c794..d57f621 100644 --- a/source/ucla-miniscope-v4/user/assembly/objective.rst +++ b/source/ucla-miniscope-v4/user/assembly/objective.rst @@ -24,11 +24,13 @@ Insert 1st Lens #. Position first lens convex-up on lens tissue paper on work surface. Confirm the lens does not wobble when laterally perturbed. Concentrically align the objective module's bore with the optical axis of the first lens +.. .. image:: first-lens-objective-aligned.webp :alt: image of first lens objective aligned #. Press objective module down and over first lens until the objective module is flush with work surface. Gentle force is acceptable provided that the lens and objective module maintain parallel alignment through the pressing process +.. .. image:: first-lens-objective-flush.webp :alt: image of first lens objective flush @@ -37,6 +39,7 @@ Insert 1st Lens #. Pre-screw 3 screws on objective module without protruding +.. .. image:: three-screws.webp :alt: image of three screws @@ -45,6 +48,7 @@ Insert 1st Lens #. Clean bottom edge of lens with lens cloth +.. .. image:: clean-1st-lens.webp :alt: image of cleaning 1st lens @@ -54,16 +58,19 @@ Insert 2nd Lens #. Insertion of the first lens sometimes introduces burrs. If those burrs are not loose, use forceps to remove them; do not scratch lens in this process. If those burrs are loose, gently tap the objective module against the work surface such that they fall out. Confirm that there are no burrs in the optical path before proceeding. Such burrs interfere image formation and are more difficult to remove after the following steps are carried out. -.. image:: objective-module-burr-inspection.webp +.. + .. image:: objective-module-burr-inspection.webp :alt: image of inspecting and removing burrs #. Position second lens convex-up on lens tissue paper on work surface. Confirm the lens does not wobble when laterally perturbed. Concentrically align the objective module's bore with the optical axis of the second lens +.. .. image:: second-lens-objective-aligned.webp :alt: image of first lens objective #. Press objective module down and over second lens until the objective module is flush with work surface. Gentle force is acceptable provided that the lens and objective module maintain parallel alignment through the pressing process +.. .. image:: second-lens-objective-flush.webp :alt: image of first lens objective diff --git a/source/ucla-miniscope-v4/user/assembly/pcb.rst b/source/ucla-miniscope-v4/user/assembly/pcb.rst index 8a23a5b..75d2cb4 100644 --- a/source/ucla-miniscope-v4/user/assembly/pcb.rst +++ b/source/ucla-miniscope-v4/user/assembly/pcb.rst @@ -3,7 +3,8 @@ PCB ### -.. image:: ucla-miniscope-v4-pcb-flaps.webp +.. + .. image:: ucla-miniscope-v4-pcb-flaps.webp :alt: image of UCLA Miniscope v4 PCB flaps *********** @@ -12,7 +13,8 @@ Preparation #. If your UCLA Miniscope v4 PCB has tabs on the ETL/EWL rings, cut those tabs off -.. image:: ucla-miniscope-v4-tabs.webp +.. + .. image:: ucla-miniscope-v4-tabs.webp :alt: image of without tabs *************************************** @@ -24,12 +26,14 @@ Fasten the Excitation Module to the PCB #. Insert two ____ screws for fastening the PCB to the excitation module into the two holes that are located on the LED/EWL flap of the PCB -.. image:: ucla-miniscope-v4-excitation-holes.webp +.. + .. image:: ucla-miniscope-v4-excitation-holes.webp :alt: image of without tabs #. Fit the LED/EWL flap of the PCB onto excitation module. Finish screwing the two screws into the excitation module, securing the excitation module against the PCB -.. image:: ucla-miniscope-v4-excitation-module-fastened.webp +.. + .. image:: ucla-miniscope-v4-excitation-module-fastened.webp :alt: image of without tabs ************************************************** diff --git a/source/ucla-miniscope-v4/user/assembly/preparation.rst b/source/ucla-miniscope-v4/user/assembly/preparation.rst index e157ba6..4523922 100644 --- a/source/ucla-miniscope-v4/user/assembly/preparation.rst +++ b/source/ucla-miniscope-v4/user/assembly/preparation.rst @@ -7,15 +7,18 @@ Preparation #. Gather the tools necessary for miniscope assembly +.. .. image:: necessary-tools.webp :alt: image of necessary tools #. Gather the UCLA Miniscope v4's constituent parts +.. .. image:: ucla-miniscope-v4-parts.webp :alt: image of miniscope's parts #. Scrape burrs from Delrin parts +.. .. image:: scrape-burrs.webp :alt: image of scraping burrs diff --git a/source/ucla-miniscope-v4/user/assembly/validate-finish.rst b/source/ucla-miniscope-v4/user/assembly/validate-finish.rst index daa31cd..b15e10b 100644 --- a/source/ucla-miniscope-v4/user/assembly/validate-finish.rst +++ b/source/ucla-miniscope-v4/user/assembly/validate-finish.rst @@ -23,10 +23,12 @@ Finish #. Secure the UCLA Miniscope v4 upside down with tape, in a vise, or between fingers -.. image:: ucla-miniscope-v4-secured-upside-down.webp +.. + .. image:: ucla-miniscope-v4-secured-upside-down.webp :alt: image of UCLA Miniscope v4 secured upside down #. Glue one side at a time without excess (first side without PCB, then next side, then final side) and let cure completely -.. image:: ucla-miniscope-v4-glue.webp +.. + .. image:: ucla-miniscope-v4-glue.webp :alt: image of UCLA Miniscope v4 getting glued \ No newline at end of file