Messages

31

Data Analysis / Re: pre-processing

« on: March 23, 2018, 04:25:41 PM »

Hi Joma,
We often spatially downsample by 2 when running analysis. I would suggest using the CaImAn package, https://github.com/flatironinstitute/CaImAn, and not the analysis code I have up on GitHub. The CaImAn package has some parameters to do downsampling as well.

32

Data Analysis / Re: msRun Error

« on: February 28, 2018, 09:45:50 PM »

Hi Kyuhyun,
It looks like the error is coming up when you try and process the behavior video. Did you record behavior on a separate webcam in this recording session?

I would recommend moving away from the old analysis code on my GitHub and instead working with the CaImAn package, https://github.com/flatironinstitute/CaImAn.

33

Optics / Re: discussion about prism

« on: February 23, 2018, 10:29:25 PM »

Hi,
I think there is a just a bit of confusion. It sounds like they think you are asking about making a GRIN prism instead of making a GRIN lens that a glass prism will be mounted to. You should generate a drawing with as much detail as possible to clarify.

34

Optics / Re: discussion about prism

« on: February 22, 2018, 06:13:52 PM »

Hi Chenglin,
You should be able to can contact Grintech and give them the dimensions of the prism you want to use and they will calculate the needed pitch. That being said, pushing the working distance of the lens +2mm might be a bit much. Since the field of view of the Miniscope is under 1mm x 1mm you might want to consider using a 1mm prism.

35

System Assembly Troubleshooting / Re: Could I get some tips for soldering coaxial cables?

« on: December 14, 2017, 07:16:17 PM »

Hi Haram,
I have never actually done this version of the soldering so I don't have pictures to show you. Maybe someone else can post their setup.

Basically you are replacing the direct solder connection of the coax cable onto the CMOS PCB with a male and female millmax connector. The connector has 2 pins: one connects to the internal signal wire of the coax cable and the other connects to the outer grounded shield of the coax cable.

36

DAQ Software/Firmware / Re: MSCam Frame Retrieve Error

« on: December 13, 2017, 10:47:14 PM »

Hi qdong8,
If the coax cable did short near the SMA connector on the DAQ PCB then there is a chance inductor L13 was fried and needs replacing. L13 can get damaged by a short and cause the exact situation you are describing... all 3 green LEDs are on on the DAQ PCB, the red and blue LED are on on the CMOS PCB, but the computer cannot establish a connection to the video stream.

37

DAQ Software/Firmware / Re: MSCam Frame Retrieve Error

« on: December 12, 2017, 05:02:33 PM »

Hi qdong8,
Yes this sounds like an issue with the soldering. Did you check for shorts on the SMA2Coax PCB before plugging it into the DAQ PCB?

38

System Assembly Troubleshooting / Re: Light leakage in miniscope body

« on: December 11, 2017, 06:31:14 PM »

Hi thkim3,
If the filter set isn't scratch and placed into the Miniscope correctly, you shouldn't have any light leakage. In an older design, using black enamel paint along the edges of the optical elements could solve light leakage but it shouldn't be necessary any more. Can you upload some pictures of your setup on imgur.com and link them here so I can have a better idea of what your setup looks like. Thanks

39

Optics / Re: Which achromatic lens to use for 1mm FOV?

« on: December 06, 2017, 08:49:53 PM »

Hi konell,
Switching to a shorter focus length achromatic lens will decrease the magnification of the system and increase your field of view. You won't likely be able to get to 1mm FOV but it should improve your current FOV by a decent amount.

Remember though, a shorter focal length lens will shift the range of depths you can image closer to the bottom surface of the GRIN lens.

40

Behavior / Re: the data acquisition software having problem when acquire both videos

« on: December 01, 2017, 05:54:16 AM »

Hi xiaoyup,
You need to select an ROI for the behavioral video stream before the DAQ software allows you to record. To do this, once the DAQ software connects to the behavioral camera, click and drag your computer mouse on the behavioral camera live video to draw a rectangular ROI. Once done, the "record" button should become clickable.

I have been planning on removing the requirement for an ROI for the behavior camera but haven't gotten around to modifying the DAQ software yet.

41

Behavior / Re: Swivel/tether for hands-off recording

« on: November 22, 2017, 03:36:00 PM »

Hi AScheyer,
Take a look at the bottom of this post, http://miniscope.org/board/index.php?topic=337.msg368#msg368.

We often use 2 channel commutators from DragonFly for Miniscope recordings in mice as well.

42

DAQ Software/Firmware / Re: GPIF 2 loading error

« on: November 12, 2017, 06:02:17 PM »

Hi,
Sorry I still haven't gotten around to looking into this. I'll try to put some time aside for it soon.

43

Optics / Re: Field of view dependent on Achromatic lens?

« on: November 11, 2017, 09:37:02 PM »

Hi Ivo,
The focal length of the achromatic lens changes the overall magnification of the Miniscope system. There is a decrease of about 30% of FOV area when going between a 12.5mm focal length lens and a 20mm focal length lens. The longer the focal length, the smaller the FOV will be. You can use a resolution calibration test slide to get exact numbers.

44

Electronics / Re: Controlling a second LED (Optogenetics)

« on: November 11, 2017, 09:35:29 PM »

Hi Ivo,
Yes it is but it requires a different LED PCB and also will require a slight change in the firmware running on the DAQ PCB. I haven't fully tested out our 2 LED system yet but I would be happy to share with you everything we have done so far. Shoot me an email when/if you are interested (DBAharoni@gmail.com).

45

Data Analysis / Re: Undefined function or variable 'C1'.

« on: October 31, 2017, 03:33:21 PM »

Hi Dechuan,
This error looks to be coming from fast_oopsi which is the non-negative decovolution code from the Paninski lab. I'm not familiar with the source of this error. Our analysis code is pretty outdated on our github repo and I would suggest you switch over to using a fully analysis package from the Paninski lab, https://github.com/simonsfoundation/CaImAn. I think they are in the process of adding in CNMF_E for 1P imaging but it is already a really great place to start.