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Messages - Jesper.vernooij

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About msRasterPlot: deconvoluted calcium bursts are depicted with a red line with or without a black lined centre.
    Q: What doe the Red and Black line represent? (what is the difference between a red line with and without a black lined centre?)

Thank you!

DAQ Software/Firmware / Re: dropped frames
« on: October 31, 2016, 09:28:39 PM »
Hi Daniel, We have just ordered an crucial SSD for the laptop. I will make an update once I have recorded data with the new drive! Thank you for the suggestion.

DAQ Software/Firmware / Re: dropped frames
« on: October 28, 2016, 11:46:41 PM »
Hi Daniel,

Thank you for the detailed information! I have checked to see if reducing the Behavior ROI has effect on the frame buffer errors and it does indeed (smaller ROI == less errors). Unfortunately our setup has some limits regarding the height of the camera, so getting the ROI smaller than it is now is not an option without getting a new camera. The write speed is fine when only imaging neurons, but with the behavior camera (no matter how small the ROI) the hard drive can't manage.

I am thinking of upgrading the computer with an m2.2280 sata SSD and put the savefile folder on that partition, which would increase my write speed to 510 mb/s. I'll let you know if it fixes the problem!


DAQ Software/Firmware / Re: dropped frames
« on: October 27, 2016, 10:19:56 PM »
Hi Stephan/Daniel,

I have a similar problem when imaging and recording behavior simultaneously at 30 fps both. The laptop We're using is a brand new Dell inspiron 7559 (5400 rpm drive, no ssd). All ports are USB3.

During recording error messages pop up in the dialog box mentioning both scope and behavior frame buffer errors after about 5 seconds of imaging, which looking at the resulting videos yields a mouse movement jump spanning roughly 5 seconds in the worst case to not noticeable in the best case. I've noticed that write speed for both Behavior and Scope fluctuates rapidly between 1 and 200. The fps fluctuates around 28 fps and shoots up randomly occasionally to over 2000, which seems to coincide with the frame buffer errors, but not always.

Any clue as to what might be the issue?



Hi everyone,

I'm having some issues getting the filters and lenses clean. They seem to a little bit dirty out of the box and whatever I do to clean them, I only seem to make matters worse. Does anyone have a simple cleaning method that does the job?

Thank you,


Thank you very much Daniel!

I'll look into the deconvlucy() function if I can't get fast-oopsi to work and post my results if any.

Hi everybody,

We have recently gotten some sessions with neurons popping up, therefore we have delved into the analysis part of the miniscope. All the standard functions in msRunBatch and msRun seem to work fine up till ms = msExtractFiring(ms); where I get the following error:

>> ms = msExtractFiring(ms);
Undefined function or variable 'C1'.

Error in fast_oopsi/est_MAP (line 305)
                C    = C1;                      % update C

Error in fast_oopsi (line 165)
[n C posts(1)] = est_MAP(F,P);

Error in msExtractFiring (line 25)
    [n_best p_best V2 C] = fast_oopsi(F,V,P);

Does anyone know how to fix this? I assume C1 is not produced by the while loop in est_MAP where it should be produced because of some reason. It it perhaps because of some of the thresholds or ROIs I have set? Can I just uncomment the msExtractFiring and still get a meaningful ms.mat?

Other basic questions (I might have already asked them on the old forum, but it might be good to have the answers here as well):
 1- What features are important when selecting the threshold for ms = msSelectFluorThresh(ms), ROIs in ms = msSelectROIs(ms), the mean frame in ms = msMeanFrame(ms,downsample), the best alignment in ms = msSelectAlignment(ms);.
 2- Once all current processing functions are ran, which parameters contain what information? (important ones, like post-proc traces for all segments, ).
 3- Is there a function that creates a video file of the processed traces, like the one on the main page of the miniscope website?

I'm sorry for the amount of questions for one post, but I hope the answers will benefit all :)

Thank you,


Electronics / Re: Flickering excitation LED with longer coax cable
« on: August 12, 2016, 08:15:37 PM »
Thanks for all the tips! I replaced the LED and everything works fine now. Must have indeed been damage from the solder job.

Electronics / Flickering excitation LED with longer coax cable
« on: August 11, 2016, 08:51:02 PM »
Hi Everyone,

We have recently build a new miniscope featuring a 4' (~1,21m) coax cable. All components work as they should but the excitation LED flickers in strength quite some. In addition, whenever we connect our older miniscopes, the LED shines a little bit on 0% excitation power. The new LED first turns on at 20% power. For a full image: the older working miniscopes feature roughly 1,5' (45cm) cables. Does anyone know if the length of the cable is a factor in excitation LED power output and stability? Or did I just do a bad job soldering?



Hi Austin, We had similar problems at the beginning. Tried a lot to get it to work, re-soldering and sorts. In the end it turned out that on that particular computer the DAQ always booted with a frame retrieve error. Simply clicking connect again solved the problem. This computer (Dell i7 desktop) however was quite unstable, often resulting in a red screen after a couple of seconds independent of parts movement. I then tried it out on my own labtop (dell inspiron 7559) and the system runs completely faultless on that system. We ended up buying the same labtop for the lab aswell.

TLDR: The specific computer one uses for some reason influences one's connection, try multiple computers before doing invasive troubleshooting.   :)

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