Recent Posts

91

Data Analysis / Re: Sample Workshop data stats

« Last post by kjlawlor on April 02, 2018, 09:06:12 PM »

Could you please provide the link for the workshop sample data? I tried finding/ downloading it but I have an error when clicking on the sample data link on the Online Workshop page (https://ucla.box.com/s/qd4aikyy1tk3iciqgfx73urr6dcc45mv%7C). Thank you!

92

DAQ Software/Firmware / Re: Error recognizing USB. Install failed.

« Last post by pcooper on March 28, 2018, 07:51:38 PM »

Hi Daniel,

Thanks for taking the time to reply.

I've tried it with 2 seperate USB 3.0 cables, one USB 2 cable, and 3 seperate computers (Win10, Win7, unsure of MacOS version). Each computer is a single OS only. All computers and cables work normally with any other task and equipment.

The soldering concern was only with the 2 pins on either side of the chip that don't have any noticable solder fillet. The other 10 look as good as a lead-free reflow can.

I've since reached out to LabMaker. They claim to have pre-installed the firmware. Working with them to further troubleshoot now.

Is there something I don't know about USB 3.0 that would allow the cables to work perfectly with an external HDD but not with this? Both cables tested are 1m long or shorter. I'll try more if you think it's worth the time, but I'm having a hard time understanding what difference could be made.

93

DAQ Software/Firmware / Re: which version of visual studio the MiniscopeControl was compiled?

« Last post by Daniel Aharoni on March 28, 2018, 06:04:53 PM »

Hi Richardson,
I wrote the DAQ software using Visual Studio 2012.

94

DAQ Software/Firmware / Re: Capturing miniscope data with micromanager

« Last post by Daniel Aharoni on March 28, 2018, 06:03:59 PM »

Hi,
We haven't tried using micromanager but I think it would be possible. The Miniscope shows up as a generic webcam to the computer so as long as micromanager can stream in a webcam video (using the standard UVC protocol) then it should work.

95

DAQ Software/Firmware / Re: Running 2 DAQ Boards on the same Workstation

« Last post by Daniel Aharoni on March 28, 2018, 06:01:42 PM »

Hi Ivo,
As long as your USB3 driver and computer hardware can handle the bandwidth of 2 Miniscopes you should be able to run 2 at the same time on the same computer.

96

DAQ Software/Firmware / Re: Error recognizing USB. Install failed.

« Last post by Daniel Aharoni on March 28, 2018, 05:55:54 PM »

Hi Phil,
From what I understand LabMaker tests their boards before shipping them out and has already performed the EEPROM programming through the board. You should contact them to double check that this is the case and that they were able to get it to function properly.

The soldering looks alright to me. I would suggest buying a couple different USB cables first and see if that is the issue. Are you running Windows 7 through Bootcamp on your Mac? Parallels won't work.

97

DAQ Software/Firmware / Error recognizing USB. Install failed.

« Last post by pcooper on March 26, 2018, 07:37:31 PM »

Hello,

I cannot get my DAQ to be recognized by my computer to begin the firmware install.

I have a "MINISCOPE USB_Control v2.3" board. Came with all through hole components and EEPROM installed from LabMaker.

When plugged in with a known good USB 3 cable, it either acts as if nothing has been plugged in (Win7, Mac) or gives a hardware error (Win10). Win10 error screen shot attached.

I have double checked all switch settings per the setup guide. http://miniscope.org/index.php/Data_Acquisition_Box#Firmware
Jumpers are in K1, K2, and J9-USB.
I have swapped out the EEPROM with no difference in results.

I'm hoping there may be something I'm missing. I'm starting to worry I got a bad board. Some of the solder joints look a little starved. (U6 especially. pics attached).

Any thoughts on what I could be doing wrong? If not, any insight on how good LabMaker is about replacements?

Thanks,
Phil

98

Data Analysis / Re: pre-processing

« Last post by Daniel Aharoni 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.

99

Data Analysis / pre-processing

« Last post by Joma on March 21, 2018, 06:58:50 PM »

Is there a way to downsample the video clips before starting the analysis suite?
I was thinking about binning - spatial downsampling - by a factor of 2 in each dimension (averaging across neighboring pixels).
what parameters in the code need to be changed? Bounderies of segments should be adjusted to the new frame dimensions, I guess.

best,

Joe

100

Data Analysis / Re: Does the downloadable Matlab code here using CNMF-E algorithm?

« Last post by Honi on March 20, 2018, 04:04:56 PM »

No, it does not.  The CNMF-E code is available on github.  https://github.com/flatironinstitute/CaImAn/ is the python version, and https://github.com/flatironinstitute/CaImAn-MATLAB is the matlab version, which is extended here https://github.com/zhoupc/CNMF_E.