http://miniscope.org/api.php?action=feedcontributions&user=Bastijn&feedformat=atomUCLA Miniscope - User contributions [en]2024-03-29T12:12:45ZUser contributionsMediaWiki 1.27.7http://miniscope.org/index.php?title=Miniscope_Baseplate_and_Protective_Cone_for_Rats&diff=1717Miniscope Baseplate and Protective Cone for Rats2018-01-29T15:13:19Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
We have developed an adjusted baseplate to hold a protective cone together with Joop Bos (NIN). Using this setup, it is possible to image in rats, while preventing damage due to grooming, bumping into objects, or other unforeseen movements. This system has successfully been tested and used in our experiments. It is possible to hold the animal while snapping on the protective cone with your other hand. Importantly, during baseplating, keep in mind that the set screw of the baseplate is oriented posterior to the animal (to its back). This way, one can easily loosen and tighten this screw and put on the protective cone from the anterior (front) side of the animal, thereby preventing the animal to take it of itself.<br />
<br />
The adjusted baseplate has to be milled, similar to the original baseplate. Keep in mind that the height of the baseplate has increased (to 3 mm). Therefore, this system is only useful in combination with a GRIN relay lens. In addition, we have put the set screw in the center to hold the LED PCB rather than the Miniscope housing, as the housing is more fragile. Finally, one has to glue three magnets into the holes, similar to the original baseplate.<br />
<br />
The protective cone consists of two parts, left and right, which have to be hold together by an iron rod or thick wire. We have successfully printed both parts using a standard Ultimaker 3D printer, but advice to use a printer with higher resolution as it increases precision (to snap together left and right) and strength (although no protective cone has been damaged during experiments). <br />
<br />
Finally, we noticed that rats can take off the protective cap quite easily (within a few days). Therefore, we slightly adjusted the protective cap so it fits better.<br />
<br />
<br />
[[File:Stages prot cone.jpg|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl and .stp files to directly 3D print (protective cone) or mill the adjusted baseplate, respectively.<br />
<br />
[[Media:ProtectiveConeRat.zip|Baseplate and Protective Cone Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Baseplate_and_Protective_Cone_for_Rats&diff=1716Miniscope Baseplate and Protective Cone for Rats2018-01-29T15:11:46Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
We have developed an adjusted baseplate to hold a protective cone together with Joop Bos (NIN). Using this setup, it is possible to image in rats, while preventing damage due to grooming, bumping into objects, or other unforeseen movements. This system has successfully been tested and used in our experiments. It is possible to hold the animal while snapping on the protective cone with your other hand. Importantly, during baseplating, keep in mind that the set screw of the baseplate is oriented posterior to the animal (to its back). This way, one can easily loosen and tighten this screw and put on the protective cone from the anterior (front) side of the animal, thereby preventing the animal to take it of itself.<br />
<br />
The adjusted baseplate has to be milled, similar to the original baseplate. Keep in mind that the height of the baseplate has increased (to 3 mm). Therefore, this system is only useful in combination with a GRIN relay lens. In addition, we have put the set screw in the center to hold the LED PCB rather than the Miniscope housing, as the housing is more fragile. Finally, one has to glue three magnets into the holes, similar to the original baseplate.<br />
<br />
The protective cone consists of two parts, left and right, which have to be hold together by an iron rod or thick wire. We have successfully printed both parts using a standard Ultimaker 3D printer, but advice to use a printer with higher resolution as it increases precision (to snap together left and right) and strength (although no protective cone has been damaged during experiments). <br />
<br />
Finally, we noticed that rats can take of the protective cap quite easily (within a few days). Therefore, we slightly adjusted the protective cap so it fits better.<br />
<br />
<br />
[[File:Stages prot cone.jpg|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl and .stp files to directly 3D print (protective cone) or mill the adjusted baseplate, respectively.<br />
<br />
[[Media:ProtectiveConeRat.zip|Baseplate and Protective Cone Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1715Miniscope Gripper2018-01-29T14:20:57Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
Together with Ralph Hamelink (NIN), we have developed a Miniscope gripper that can be 3D printed with low and high resolution printers. The gripper allows to hold the Miniscope during baseplating. This is especially convenient when imaging deep brain regions, thereby having a GRIN relay lens implanted. The gripper has been tested successfully during multiple baseplate surgeries. <br />
<br />
Use the "Miniscope gripper - High resolution printing.stl" file if you have access to a high resolution printer (e.g., SLA printing). Use a m3 screw to clamp the miniscope. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
Use the "Miniscope gripper - Low resolution printing.stl" file if you have a low resolution printer (e.g., Ultimaker). Tap m3 thread into the side hole of the gripper (use an 2.65mm drill). Use a m3 screw to hold the miniscope. Tap m5 thread into the top of the gripper (use a 4.5mm drill). Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
<br />
[[File:GripperExample.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=File:GripperExample.png&diff=1714File:GripperExample.png2018-01-29T14:20:19Z<p>Bastijn: </p>
<hr />
<div></div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1713Miniscope Gripper2018-01-29T14:19:38Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
Together with Ralph Hamelink (NIN), we have developed a Miniscope gripper that can be 3D printed with low and high resolution printers. The gripper allows to hold the Miniscope during baseplating. This is especially convenient when imaging deep brain regions, thereby having a GRIN relay lens implanted. The gripper has been tested successfully during multiple baseplate surgeries. <br />
<br />
Use the "Miniscope gripper - High resolution printing.stl" file if you have access to a high resolution printer (e.g., SLA printing). Use a m3 screw to clamp the miniscope. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
Use the "Miniscope gripper - Low resolution printing.stl" file if you have a low resolution printer (e.g., Ultimaker). Tap m3 thread into the side hole of the gripper (use an 2.65mm drill). Use a m3 screw to hold the miniscope. Tap m5 thread into the top of the gripper (use a 4.5mm drill). Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm. Miniscope Gripper<br />
<br />
<br />
[[File:GripperExample.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=File:Miniscope_Gripper.png&diff=1712File:Miniscope Gripper.png2018-01-29T14:18:35Z<p>Bastijn: Bastijn uploaded a new version of File:Miniscope Gripper.png</p>
<hr />
<div></div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1711Miniscope Gripper2018-01-29T14:11:56Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
Together with Ralph Hamelink (NIN), we have developed a Miniscope gripper that can be 3D printed with low and high resolution printers. The gripper allows to hold the Miniscope during baseplating. This is especially convenient when imaging deep brain regions, thereby having a GRIN relay lens implanted. The gripper has been tested successfully during multiple baseplate surgeries. <br />
<br />
Use the "Miniscope gripper - High resolution printing.stl" file if you have access to a high resolution printer (e.g., SLA printing). Use a m3 screw to clamp the miniscope. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
Use the "Miniscope gripper - Low resolution printing.stl" file if you have a low resolution printer (e.g., Ultimaker). Tap m3 thread into the side hole of the gripper (use an 2.65mm drill). Use a m3 screw to hold the miniscope. Tap m5 thread into the top of the gripper (use a 4.5mm drill). Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
<br />
[[File:Miniscope Gripper.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1710Miniscope Gripper2018-01-29T14:09:36Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
Together with Ralph Hamelink (NIN), we have developed a Miniscope gripper that can be 3D printed with low and high resolution printers. The gripper allows to hold the Miniscope during baseplating. This is especially convenient when imaging deep brain regions, thereby having a GRIN relay lens implanted. The gripper has been tested successfully during multiple baseplate surgeries. <br />
<br />
Use the "Miniscope gripper - High resolution printing.stl" file if you have access to a high resolution printer (e.g., SLA printing). Use a m3 screw to clamp the miniscope. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
Use the "Miniscope gripper - Low resolution printing.stl" file if you have a low resolution printer (e.g., Ultimaker). Tap m3 thread into the side hole of the gripper. Use a m3 screw to hold the miniscope. Tap m5 thread into the top of the gripper. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
<br />
[[File:Miniscope Gripper.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1709Miniscope Gripper2018-01-29T14:09:19Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
Together with Ralph Hamelink (NIN), we have developed a Miniscope gripper that can be 3D printed with low and high resolution printers. The gripper allows to hold the Miniscope during baseplating. This is especially convenient when imaging deep brain regions, thereby having a GRIN relay lens implanted. The gripper has been tested successfully during multiple baseplate surgeries. <br />
<br />
Use the "Miniscope gripper - High resolution printing.stl" file if you have access to a high resolution printer (e.g., SLA printing). Use a m3 screw to clamp the miniscope. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
Use the "Miniscope gripper - Low resolution printing.stl" file if you have a low resolution printer (e.g., Ultimaker). Tap m3 thread into the side hole of the gripper. Use a m3 screw to hold the miniscope. Tap m5 thread into the top of the gripper. Take an aluminium rod (~6mm in diameter) and tap thread onto the rod. This can be screwed on top of the gripper and can be used to attach the gripper to the stereotaxic arm.<br />
<br />
[[File:Miniscope Gripper.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Gripper&diff=1708Miniscope Gripper2018-01-29T13:56:46Z<p>Bastijn: /* Downloads */</p>
<hr />
<div>== Description ==<br />
<br />
[[File:Miniscope Gripper.png|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl files and 3D drawings here.<br />
<br />
[[Media:Miniscope Gripper.zip|Miniscope Gripper Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Other_Open_Source_Projects&diff=1694Other Open Source Projects2017-11-07T07:12:22Z<p>Bastijn: /* Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN */</p>
<hr />
<div>Listed below are open-source projects being tackled by other groups. <br />
<br />
== Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==<br />
Description, pictures, drawings, and part files for a Miniscope baseplate and protective cone.<br />
<br />
[[Miniscope Baseplate and Protective Cone for Rats]]<br />
<br />
== Miniscope Bonsai Package by Jon Newman ==<br />
"Bonsai package for controlling and acquiring data from headborne miniscopes for calcium imaging"<br />
<br />
[https://github.com/jonnew/Bonsai.Miniscope Bonsai.Miniscope]<br />
<br />
== Constrained Nonnegative Matrix Factorization for microEndoscopic data ==<br />
Analysis package for (1) identifying spatial footprints of all neurons and (2) denoising, demixing and deconvolving the temporal signals.<br />
<br />
[[CNMF-E]]<br />
https://github.com/zhoupc/CNMF_E<br />
<br />
== Miniature Microscope from the Gardner Lab at Boston University ==<br />
[[Gardner Lab Miniature Microscope]]<br />
<br />
== Open-Ephys ==<br />
"A team of neuroscientists who want to change the way our tools are developed and shared."<br />
<br />
[http://www.open-ephys.org/ Open Ephys]<br />
<br />
== OpenMaze ==<br />
"Open source hardware and software for behavioral neuroscience. Learn how to design and build fully functional animal behavioral setups rapidly, cheaply, and easily."<br />
<br />
[http://claylacefield.wix.com/openmazehome OpenMaze]<br />
<br />
== Open Behavior ==<br />
"Open Behavior is dedicated to accelerating behavioral neuroscience research through the promotion of collaboration and open-source projects."<br />
<br />
[http://openbehavior.com/ Open Behavior]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Baseplate_and_Protective_Cone_for_Rats&diff=1693Miniscope Baseplate and Protective Cone for Rats2017-11-07T07:11:25Z<p>Bastijn: /* Description */</p>
<hr />
<div>== Description ==<br />
We have developed an adjusted baseplate to hold a protective cone together with Joop Bos (NIN). Using this setup, it is possible to image in rats, while preventing damage due to grooming, bumping into objects, or other unforeseen movements. This system has successfully been tested and used in our experiments. It is possible to hold the animal while snapping on the protective cone with your other hand. Importantly, during baseplating, keep in mind that the set screw of the baseplate is oriented posterior to the animal (to its back). This way, one can easily loosen and tighten this screw and put on the protective cone from the anterior (front) side of the animal, thereby preventing the animal to take it of itself.<br />
<br />
The adjusted baseplate has to be milled, similar to the original baseplate. Keep in mind that the height of the baseplate has increased (to 3 mm). Therefore, this system is only useful in combination with a GRIN relay lens. In addition, we have put the set screw in the center to hold the LED PCB rather than the Miniscope housing, as the housing is more fragile. Finally, one has to glue three magnets into the holes, similar to the original baseplate.<br />
<br />
The protective cone consists of two parts, left and right, which have to be hold together by an iron rod or thick wire. We have successfully printed both parts using a standard Ultimaker 3D printer, but advice to use a printer with higher resolution as it increases precision (to snap together left and right) and strength (although no protective cone has been damaged during experiments). <br />
<br />
<br />
[[File:Stages prot cone.jpg|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl and .stp files to directly 3D print (protective cone) or mill the adjusted baseplate, respectively.<br />
<br />
[[Media:ProtectiveConeRat.zip|Baseplate and Protective Cone Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Miniscope_Baseplate_and_Protective_Cone_for_Rats&diff=1692Miniscope Baseplate and Protective Cone for Rats2017-11-07T06:57:41Z<p>Bastijn: /* Downloads */</p>
<hr />
<div>== Description ==<br />
[[File:Stages prot cone.jpg|center|600px]]<br />
<br />
== Downloads ==<br />
Download the .stl and .stp files to directly 3D print (protective cone) or mill the adjusted baseplate, respectively.<br />
<br />
[[Media:ProtectiveConeRat.zip|Baseplate and Protective Cone Files]]</div>Bastijnhttp://miniscope.org/index.php?title=Member_Pages&diff=1590Member Pages2017-01-31T07:14:52Z<p>Bastijn: /* Europe */</p>
<hr />
<div>Below is a list of miniscope.org member created pages. These pages are a place for community members to share their contact information, current work, interests, and whatever else they find relevant. A major goal of miniscope.org is to foster an environment of open sharing, communication, and collaboration.<br />
<br />
'''We highly encourage all miniscope.org members to add their information below.''' You can reach your own member page by clicking your account name at the top right of the page or by going to "http://miniscope.org/index.php?title=User:XXXX", replacing 'XXXX' with your user name. Member pages can be modified by that member without needing approval by an administrator. If you would like to add a link to your member page here, please do so by editing this page or posting a thread on the discussion board.<br />
<br />
== Miniscope Team ==<br />
{| class="wikitable"<br />
|-<br />
! scope="col"| Name<br />
! scope="col"| Member Page<br />
! scope="col"| Lab<br />
! scope="col"| University<br />
|-<br />
! Daniel Aharoni<br />
| [[User:DAharoni|DAharoni]]<br />
| Golshani, Silva, Khakh<br />
| UCLA<br />
|-<br />
! Tristan Shuman<br />
| [[User:Tristanshuman|Tristanshuman]]<br />
| Golshani<br />
| UCLA<br />
|-<br />
! Denise Cai<br />
| [[User:Denisecai|Denisecai]]<br />
| Silva<br />
| UCLA<br />
|-<br />
! Tsai-Yi Lu<br />
| [[User:tsaiyilu|tsaiyilu]]<br />
| Khakh<br />
| UCLA<br />
|-<br />
! Mimi La-Vu<br />
| [[User:MyQLaVu|MyQLaVu]]<br />
| Silva<br />
| UCLA<br />
|}<br />
<br />
== Miniscope.org Community Members ==<br />
=== Americas ===<br />
{| class="wikitable"<br />
|-<br />
! scope="col"| Name<br />
! scope="col"| Member Page<br />
! scope="col"| Lab<br />
! scope="col"| University<br />
|-<br />
! Stephen Johnston<br />
| [[User:johnston|johnston]]<br />
| Gage<br />
| Salk<br />
|-<br />
! Walter Gonzalez<br />
| [[User:Walter|Walter]]<br />
| Lois<br />
| Caltech<br />
|-<br />
! Alberto Sepulveda<br />
| [[User:Asr|Asr]]<br />
| Forcelli<br />
| Georgetown University<br />
|-<br />
! Najet Serradj <br />
| [[User:Nserradj|Nserradj]]<br />
| Hollis<br />
| Burke<br />
|-<br />
! Jesper Vernooij<br />
| [[User:Jesper.Vernooij|Jesper.Vernooij]]<br />
| Leutgeb S.<br />
| University of California San Diego<br />
|-<br />
! Keiland Cooper<br />
| [[User:kwcooper|kwcooper]]<br />
| Newman<br />
| Indiana University<br />
|-<br />
!Casey Vickstrom<br />
| [[User:Cvickstrom|Cvickstrom]]<br />
| Liu<br />
| Medical College of Wisconsin<br />
|}<br />
<br />
=== Europe ===<br />
{| class="wikitable"<br />
|-<br />
! scope="col"| Name<br />
! scope="col"| Member Page<br />
! scope="col"| Lab<br />
! scope="col"| University<br />
|-<br />
! Nikolas Karalis<br />
| [[User:Nikolas|Nikolas]]<br />
| Sirota<br />
| LMU<br />
|-<br />
<br />
! Tycho Hoogland<br />
| [[User:Hoogland|Hoogland]]<br />
|<br />
| Erasmus MC<br />
|-<br />
! Christophe Lamy<br />
| [[User:Clamy|Lamy]]<br />
| Lamylab<br />
| University of Fribourg<br />
<br />
! Bastijn van den Boom<br />
| [[User:Bastijn|Bastijn]]<br />
| Willuhnlab<br />
| Netherlands Institute for Neuroscience<br />
|-<br />
|}<br />
<br />
=== Asia ===<br />
{| class="wikitable"<br />
|-<br />
! scope="col"| Name<br />
! scope="col"| Member Page<br />
! scope="col"| Lab<br />
! scope="col"| University<br />
|-<br />
! Roman Boehringer<br />
| [[User:Roman|Roman]]<br />
| McHugh<br />
| Riken BSI<br />
|-<br />
! Ryosuke Enoki<br />
| [[User:Enoki|Enoki]]<br />
| Honma<br />
| Hokkaido Univ<br />
|-<br />
! Yusuke Seto<br />
| [[User:Seto|Seto]]<br />
| Matsuo<br />
| Osaka Univ<br />
|-<br />
! Yuichiro Hayashi<br />
| [[User:Yhayashi|Yhayashi]]<br />
| <br />
| Hokkaido Univ<br />
|-<br />
|-<br />
! Euiheon Chung<br />
| [[User:Ogong50|Ogong50]]<br />
| BiOscopy Lab<br />
| Gwangju Institute of Science and Technology<br />
|-<br />
|}</div>Bastijnhttp://miniscope.org/index.php?title=User:Bastijn&diff=1589User:Bastijn2017-01-31T07:12:11Z<p>Bastijn: </p>
<hr />
<div>Bastijn van den Boom<br />
<br />
Willuhnlab<br />
<br />
Netherlands Institute for Neuroscience</div>Bastijnhttp://miniscope.org/index.php?title=User:Bastijn&diff=1588User:Bastijn2017-01-31T07:11:20Z<p>Bastijn: </p>
<hr />
<div>Bastijn van den Boom<br />
Willuhnlab<br />
Netherlands Institute for Neuroscience</div>Bastijnhttp://miniscope.org/index.php?title=User:Bastijn&diff=1587User:Bastijn2017-01-31T07:10:59Z<p>Bastijn: Created page with "! Bastijn van den Boom | Bastijn | Willuhnlab | Netherlands Institute for Neuroscience |-"</p>
<hr />
<div>! Bastijn van den Boom<br />
| [[User:Bastijn|Bastijn]]<br />
| Willuhnlab<br />
| Netherlands Institute for Neuroscience<br />
|-</div>Bastijn