http://miniscope.org/api.php?action=feedcontributions&user=Sergiof&feedformat=atomUCLA Miniscope - User contributions [en]2024-03-29T08:50:19ZUser contributionsMediaWiki 1.27.7http://miniscope.org/index.php?title=System_Assembly&diff=1045System Assembly2016-02-03T19:06:50Z<p>Sergiof: /* Head Mounted Scope Assembly */</p>
<hr />
<div>This guide will take you through the assembly of the entire miniscope system.<br />
== Head Mounted Scope Assembly ==<br />
A detailed video is soon to come.<br />
<br />
#Examine '''Main Body''' under a microscope and remove any plastic burrs and obstructions to the light paths.<br />
#Press fit magnets into the 3 holes on the bottom of the '''Main Body''' making sure the polarity of the magnets match previously assembled scopes.<br />
#Slide the '''Achromatic Lens''' down the emission path until it sits flush against the aperture ring above the emission filter slot. Inspect fit under microscope and adjust if necessary.<br />
#With the coated surface facing the incoming light, use forceps to slide the ''Excitation Filter, Dichroic Mirror, and Emission Filter''' into their respective slots until their sides are flush with the Main Body. The black edges of the filters represent which edges should be blackened.<br />
#Place the '''Half-Ball Lens''' in spherical opening (optical glue is optional). Inspect under a microscope to make sure the lens surface is flush with the plastic. Screw the Excitation LED PCB in place using 1mm self-tapping screws.<br />
#Screw the '''Filter Set Holder''' onto the '''Main Body''' using 2 to 3 1mm self-tapping screws.<br />
#Slide the '''Focusing Slider''' onto the '''Main Body'''. '''Make sure the two side holes have been tapped already with a 00-80 tap'''.<br />
#Epoxy, screw, or rubber band the '''CMOS Imaging Sensor PCB''' onto the '''Focusing Slider''' orienting the LED wires to the side of the scope with the '''Excitation LED PCB'''. <br />
<br />
[[File:ScopeAssembly2.png|center|900px]]<br />
<br clear=all><br />
<br />
=== Filter Edge Blackening (Suggested) ===<br />
While not strictly necessary, we suggest blackening the sides of the dichroic and emission filters. We have noticed that if a scope has light leakage issues (excitation light making it to the CMOS imaging sensor) blackening the dichroic and emission filters' sides fixes the issue. <br />
<br />
Optical companies may be able to blacken the sides for you but it is also easy to do yourself. We have had the most success using Rustoleum Flat Black Enamel with a thin paintbrush.<br />
#Pour a few drops of the enamel into a plastic dish and let it sit out for a few minutes to thicken. <br />
#Holding the sides of the filter with forceps carefully apply a thin layer of the enamel to the 2 sides not in contact with the forceps. <br />
#Let dry for a few minutes before setting the filter down. <br />
#Wait a couple hours for the enamel to dry further then repeat step 2 on the other 2 sides of the filter.<br />
<br />
<br />
=== Soldering LED power lines ===<br />
[[File:LEDWire.png|center|400px]]<br />
<br />
=== Baseplate Assembly ===<br />
#Inspect Baseplate for burrs.<br />
#Press fit the 3 magnets flush or slightly recessed into the Baseplate.<br />
#Tap the set screw hole with a 00-80 tap.<br />
<br />
[[File:BaseplateAssembly.png|center|400px]]<br />
<br />
== Data Acquisition System Assembly ==<br />
We generally have all surface mount (SMD) components assembled on the DAQ PCB by a third party PCB assembly house leaving only the through-hole components to be assembled in lab. It is possible to have the assembly house place both SMD and through-hole components but it is more expensive and through-hole components are relatively easy to solder. A good through-hole soldering tutorial can be found [https://learn.sparkfun.com/tutorials/how-to-solder---through-hole-soldering here].<br />
<br />
=== Through-hole component assembly ===<br />
If you decide to have the through-hole components assembled by an assembly house you can skip this section. Below is a picture highlighting the necessary through-hole components that need to be soldered in order for the DAQ PCB to function properly.<br />
<br />
[[File:DAQPCBThroughHole.png|center|600px]]<br />
<br />
*Description of components<br />
**SW4: Reset button the resets can reset the USB Host Controller<br />
**U5: EEPROM (memory that holds the DAQ firmware) socket. You can also solder the EEPROM IC directly to the board but I prefer using an IC socket so I can swap out the EEPROM if necessary<br />
**K1,2,3: Each are 2pin 0.1" headers<br />
**J9: A 3pin header used with a 2pin jumper to select power source for the microscope<br />
**J3,4,5: SMA connectors used for GPIO pins<br />
**J6: We currently solder a short coax cable with SMA connector to these pads. This will be updated soon to a replace this with a proper PCB footprint<br />
<br />
=== Setting Jumpers ===<br />
Once all SMD and through-hole components are in place the switches and jumpers need to be properly set for uploading firmware and powering the microscope.<br />
<br />
Below shows the default configuration of the 3 SMD switches on the DAQ PCB.<br />
<br />
[[File:SwitchSettings.png|center|500px]]<br />
<br />
Below shows the possible K1, K2, and K3 jumper configurations.<br />
<br />
[[File:BootMode.png|center|500px]]<br />
<br />
The scope power jumper, J9, sets the power source powering the head mounted scope. In most cases the USB power configuration should be used and no DC power supply needs to be hooked up the the DC jack on the PCB.<br />
<br />
[[File:PowerJumper.png|center|500px]]<br />
<br />
== Cable Assembly ==<br />
The cabling between the head mounted scope and DAQ hardware is only a single coaxial cable. A coaxial, or coax, cable consists of an inner conducting wire surrounded by an insulating dielectric and then outer, generally grounded, shield. In our system the inner conductor carries power along with a data link and bidirectional control channel and the outer shield needs to be grounded. Our hardware dynamically adjusts for signal attenuation and small voltage drops across the cable but carry should still be taken to minimize these loses.<br />
<br />
Properties to look for in a coax cable are<br />
*50ohm impedance. This is absolutely necessary.<br />
*Light weight and highly flexible. We like to use coax cables with an outer diameter of 1.5mm or less. It is important to note that as the diameter of the cable decreases, so does the length it can support.<br />
*Handles bandwidths up to 1GHz. For short distances this requirement can be reduced.</div>Sergiofhttp://miniscope.org/index.php?title=Main_Page&diff=1041Main Page2016-02-03T17:42:41Z<p>Sergiof: </p>
<hr />
<div>[[File:miniscopev2.JPG|thumb|300px]]<br />
Welcome to Miniscope.org Wiki! <br />
<br />
The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Stanford and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html paper in Nature Methods in 2011]. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (miniscope) has a mass of around 3 grams and uses only a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data. The goal of this wiki site is to provide a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important technology. The initial goal is to help disseminate this technology to the larger neuroscience community so that we can build a community of users that will continue to develop this technology and share on these developments. While the miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for a standard neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the [[Overview of System Components|Project Overview]] page. The Miniscope project and miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!<br />
<br />
== Current Status of Project ==<br />
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.<br />
<br />
Initial access to the miniscope.org wiki was enabled mid January, 2016.<br />
<br />
'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, and Visual Cortex using 1.8mm and 2mm diameter GRIN lenses from Grintech. While thinner GRIN lenses should theoretically be compatible with our system we have limited our initial development to larger lenses due to supply and experimental constraints. We are now actively testing thinner lenses as well as pursuing multiple avenues of GRIN lens production (More information on GRIN lenses can be found [[GRIN Lens Information|here]]).<br />
<br />
== Links to information on miniscope subsystems ==<br />
[[File:Overview_System.png|thumb|600px]]<br />
:[[Head Mounted Scope]]<br />
<br />
:[[Data Acquisition Box]]<br />
<br />
:[[Data Acquisition Software]]<br />
<br />
:[[Surgery Protocol]]<br />
<br />
:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]<br />
<br />
:[[Analysis Package]]<br />
<br />
<br clear=all><br />
== Discussion Board and FAQ ==<br />
:[[Special:WikiForum|Discussion Board]]<br />
:[[FAQs]]<br />
<br />
== Guides and Tutorials==<br />
A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.<br />
<br />
# [[Overview of System Components]]<br />
# [[Part Procurement]]<br />
# [[System Assembly]]<br />
# [[Recommended Computer Specs]]<br />
# [[Software and Firmware Setup]]<br />
# [[Surgery Protocol]]<br />
# [[Animal Behavior Guide]]<br />
<br />
== Update Log ==<br />
;02/03/2016<br />
;Updated Surgery Tools on Miniscope Master Parts List<br />
;01/28/2016<br />
:Added PCB price quotes to reference when ordering PCB fabrication and assembly through Sierra Circuits. They can be found on the [[Part Procurement]] page.<br />
;01/27/2016<br />
:'''IMPORTANT''': Updated CMOS Imaging Sensor PCB Fabrication file to newest version<br />
;01/20/2016<br />
:Updated Surgery Tools on Miniscope Master Parts List<br />
:Added GRIN lens specifications on [[GRIN Lens Information]] page<br />
:Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation<br />
:Slight modification to the Baseplate 3D model on Github<br />
;01/14/2016<br />
:Comments added to segmentation functions<br />
:Added through-hole components for DAQ PCB on Master Parts List<br />
:Added additional soldering tools on Master Parts List<br />
;01/13/2016<br />
:Added basic surgery outline<br />
:Added a picture guide for scope and Baseplate assembly<br />
;01/12/2016<br />
:Finalizing of Miniscope Master Parts List<br />
;01/10/2016<br />
:Upload of current version of all files and documents to Github<br />
;01/09/2016<br />
:Added guide to programming firmware to DAQ PCB</div>Sergiofhttp://miniscope.org/index.php?title=Main_Page&diff=964Main Page2016-01-20T21:14:46Z<p>Sergiof: </p>
<hr />
<div>[[File:miniscopev2.JPG|thumb|300px]]<br />
Welcome to Miniscope.org Wiki! <br />
<br />
The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Standford and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html paper in Nature Methods in 2011]. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (miniscope) has a mass of around 3 grams and uses only a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data. The goal of this wiki site is to provide a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important technology. The initial goal is to help disseminate this technology to the larger neuroscience community so that we can build a community of users that will continue to develop this technology and share on these developments. While the miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for a standard neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the [[Overview of System Components|Project Overview]] page. The Miniscope project and miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!<br />
<br />
== Current Status of Project ==<br />
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.<br />
<br />
Initial access to the miniscope.org wiki was enabled mid January, 2016.<br />
<br />
'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, and Visual Cortex using 1.8mm and 2mm diameter GRIN lenses from Grintech. While thinner GRIN lenses should theoretically be compatible with our system we have limited our initial development to larger lenses due to supply and experimental constraints. We are now actively testing thinner lenses as well as pursuing multiple avenues of GRIN lens production (More information on GRIN lenses can be found [[GRIN Lens Information|here]]).<br />
<br />
== Links to information on miniscope subsystems ==<br />
[[File:Overview_System.png|thumb|600px]]<br />
:[[Head Mounted Scope]]<br />
<br />
:[[Data Acquisition Box]]<br />
<br />
:[[Data Acquisition Software]]<br />
<br />
:[[Surgery Protocol]]<br />
<br />
:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]<br />
<br />
:[[Analysis Package]]<br />
<br />
<br clear=all><br />
== Discussion Board and FAQ ==<br />
:[[Special:WikiForum|Discussion Board]]<br />
:[[FAQs]]<br />
<br />
== Guides and Tutorials==<br />
A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.<br />
<br />
# [[Overview of System Components]]<br />
# [[Part Procurement]]<br />
# [[System Assembly]]<br />
# [[Recommended Computer Specs]]<br />
# [[Software and Firmware Setup]]<br />
# [[Surgery Protocol]]<br />
# [[Animal Behavior Guide]]<br />
<br />
== Update Log ==<br />
;01/20/2016<br />
:Updated Surgery Tools on Miniscope Master Parts List<br />
:Added GRIN lens specifications on [[GRIN Lens Information]] page<br />
:Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation<br />
:Slight modification to the Baseplate 3D model on Github<br />
;01/14/2016<br />
:Comments added to segmentation functions<br />
:Added through-hole components for DAQ PCB on Master Parts List<br />
:Added additional soldering tools on Master Parts List<br />
;01/13/2016<br />
:Added basic surgery outline<br />
:Added a picture guide for scope and Baseplate assembly<br />
;01/12/2016<br />
:Finalizing of Miniscope Master Parts List<br />
;01/10/2016<br />
:Upload of current version of all files and documents to Github<br />
;01/09/2016<br />
:Added guide to programming firmware to DAQ PCB</div>Sergiof