Recent Posts

41

DAQ Software/Firmware / Re: Camera not recognized

« Last post by Daniel Aharoni on July 26, 2018, 07:09:12 AM »

Hi amankapadia,
Once the EEPROM memory on the Miniscope DAQ has been programmed it will no longer show up in the Cypress Control Center but instead show up as a MINISCOPE under cameras in Device Manager. So that part seems to be working fine.

Try clicking the "Connect" button in the Miniscope software a few times in a row spaced out by a couple of seconds. If that doesn't connect your computer to the Miniscope video stream try using a different computer to see if it connects at all. There are a few other things to check..

* Make sure you are plugged into a USB3.0 port
* Make sure you have a decent quality USB3.0 cable
* Is there a chance you shorted the coax cable line in the recent past? This can cause a power surge through the L13 inductor resulting in all 3 green status LEDs lighting up but not being able to connect to the Miniscope video stream.

42

Data Analysis / Results from MIN1PIPE Analysis Pipeline?

« Last post by TBNentwig on July 26, 2018, 12:36:36 AM »

Hi All,

I am curious whether anyone has tried using the new MIN1PIPE pipeline (https://www.sciencedirect.com/science/article/pii/S221112471830826X?via%3Dihub#app2) in Matlab for analyzing miniscope recordings?

I'm coming from Python and have been trying to use the CNMF-E analyses from CaImAn and MiniscoPy. Interested to see whether MIN1PIPE provides significant benefits over the prior methods.

Any insight is appreciated.

--Todd N

43

DAQ Software/Firmware / Camera not recognized

« Last post by amankapadia on July 25, 2018, 04:25:20 PM »

Hey everyone,

I'm having trouble connecting the camera. It has worked in the past, but now I am encountering problems with the Miniscope Control and Cypress USB Control Center. Nothing shows up in the Miniscope Control or USB Control Center, but it does show up in the device manager. Additionally, all of the lights are lit up on the PCB and Miniscope. Here's a link with some screenshots that may be helpful: https://s3.amazonaws.com/beenhakkerlab/webfiles/Miniscope+Questions.pdf

Thanks for any help!

-Aman

44

Surgery and Baseplating / Re: nothing but gray

« Last post by Daniel Aharoni on July 22, 2018, 04:56:29 PM »

Hi kjlawlor,
There are a few labs I know of successfully imaging in rats. We work most closely with Tad Blair's Lab at UCLA and they are getting really nice data sets. Surgeries are a bit trickier in rats since their brains are larger than mice's but you still need to get the implanted less withing a couple 100um of the cells you want to image. Also, I know getting the correct GCaMP virus was very important. I think they had the most luck using AAV9 but you should double check with them.

Bastijn van den Boom at NIN has also had success imaging in rats.

45

Surgery and Baseplating / Re: nothing but gray

« Last post by hsiao on July 21, 2018, 07:33:55 AM »

Hi, kjlawlor

Would you mind to share your experience? Like where did you get your viruses and what kind of gene did they express?
How is the histology going?
Which lens did you use as objective and relay lens?

I had my second surgery done and would love to report the outcome 3~4 weeks later
This time I used addgene aav1 https://www.addgene.org/100843/

Thanks

46

Surgery and Baseplating / Re: nothing but gray

« Last post by kjlawlor on July 20, 2018, 09:23:59 PM »

Hi,

I am also trying to get my imaging in Rats to work. I have implanted 10 rats using two different viruses, and have yet to see anything. I am using the two lens relay system, with the implanted lens 8.4mm long for a region that is 5.5mm deep. I am wondering if there are any changes in the protocol for rats. Also, do you know people who have successfully imaged rats using the miniscope in such deep regions?

Does the miniscope team have a list of publications that are using the miniscope system?

Thanks for the help!

47

Surgery and Baseplating / Re: Rat

« Last post by kjlawlor on July 20, 2018, 09:18:30 PM »

Hi Honi,

I am also working in rats and I have had some issues. Have you been able to get it working? If so, did you make any changes to the protocol?
Also if you don't mind me asking, are you using the objective-relay 2 lens configuration? The area I am trying to image is at a depth of 5.5mm so I am wondering if anyone has had success doing deep brain imaging in rats. Thanks!

48

Surgery and Baseplating / Re: nothing but gray

« Last post by hsiao on July 20, 2018, 02:22:49 AM »

I am really appreciated your inputs.
 
Good luck on my second rat

49

Surgery and Baseplating / Re: nothing but gray

« Last post by Daniel Aharoni on July 18, 2018, 05:17:53 PM »

Hi,

The lens was above dCA1 cell body over ~500um. I should lower it further.

Yea, you should really try to keep this distance to under 300um. Even 300um is a bit large.

But here comes other questions.
1. The working distance of #64-519 is 0, so I should implant the lens as close to the cell bodies of dCA1 as possible (at least < 250 um)? If I choose a lens with a 0.2 mm WD, then it gives me more space so that I can implant the lens like 0.2mm or more above the cell bodies?

You should always implant the lens as close as possible to the cells you want to image. The lenses from Edmund have a design wavelength different than what you will be using. This wavelength affects the actual pitch and working distance of the lens. So the quoted 0 or 0.2mm WD willbe different when imaging green fluorescence. But in general you want the effective pitch of your objective lens to be slightly under 0.25.

2. The medial hippocampus is higher than the lateral. Will you tilt the lens a little bit to fit the hippocampus?

I'm not sure. A little tilt might help with imaging.

3. In the dual lens system, the wiki page uses the title "Imaging With Thin GRIN Lenses". My question is that is it necessary to use a relay lens that is thinner than the objective lens? Will there be any problems if I use a relay lens with the same diameter with the objective lens?

No, it can be the same diameter.

You might want to contact Walter Boyles at GoFoton, walter.boyles_at_gofoton(dot)com, and request a custom 2mm diameter GRIN lens made by them. If you give him the working distance you want (something like 200um on both ends of the GRIN lens) and the overall length you need he can maybe make you a single lens that will work for you. This would result in a single GRIN lens instead of stacking multiple lenses.

50

Surgery and Baseplating / Re: nothing but gray

« Last post by hsiao on July 16, 2018, 10:46:11 PM »

So I think the setup I was using is fine. However, I saw the histology slice yesterday.
It seems that my problem is the implantation.

The lens was above dCA1 cell body over ~500um. I should lower it further.

But here comes other questions.
1. The working distance of #64-519 is 0, so I should implant the lens as close to the cell bodies of dCA1 as possible (at least < 250 um)? If I choose a lens with a 0.2 mm WD, then it gives me more space so that I can implant the lens like 0.2mm or more above the cell bodies?

2. The medial hippocampus is higher than the lateral. Will you tilt the lens a little bit to fit the hippocampus?

3. In the dual lens system, the wiki page uses the title "Imaging With Thin GRIN Lenses". My question is that is it necessary to use a relay lens that is thinner than the objective lens? Will there be any problems if I use a relay lens with the same diameter with the objective lens?

Thank you!