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Topics - Jesper.vernooij

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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,


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 / 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?



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