Messages

1

System Assembly Troubleshooting / Re: Light leakage in miniscope body

« on: December 13, 2017, 09:38:37 AM »

Hi Daniel,
I found that there was a very small scratch I haven't noticed on the excitation filter. Replacing it with a new one solved the problem.
Thanks for advice!

2

System Assembly Troubleshooting / Light leakage in miniscope body

« on: December 06, 2017, 02:11:09 AM »

Hi everyone,
I have recently assembled  miniscopes and had light leakage problem, which was not detected in the miniscopes I assembled last year.
Applying black enamel paint on the filter edges helped a little but I can still see some light coming in to the CMOS sensor when I put the scope on black surface.
I confirmed that the CMOS sensor and LED parts have nothing to do with the light leakage by swapping the parts with my older miniscopes... It seems that the problem is solely coming from the body(where achromatic lens and filters go in).
The biggest difference between my older miniscopes and new miniscopes is that the inner diameter of the hole where the acromatic lens sits on. The new scopes have much bigger inner diameter than the previous ones. Could it be causing the problem?
Attaching pictures would helped but I couldn't figure out how to upload image files so I tried my best to describe the situation by word...

Thank you.
TaeHyun

3

Data Analysis / Re: Error message while running msRun

« on: September 07, 2016, 10:25:24 AM »

Thanks Daniel,

I have finally run the msRun script without any error message to the animal movement track figure!

I was expecting some sort of dF/F graph or other summary data figures, but after the message: 'Calculating animal position. 98.xxxx% done.'  , nothing happens and the script ends.

Is this normal? Or am I doing something wrong? Do I need to run another script to analyze single cell firing with behavior track?

When I typed in 'msPlayVidObj',

Error : msPlayVidObj (line 5)  for frameNum=1:downSamp:vidObj.numFrames

pops up.

4

Surgery and Baseplating / White spots(neurons?) with black background

« on: September 06, 2016, 11:10:02 AM »

Hi,

I checked my first surgery result recently (CA1), and found some strange points.

1. With most of the mice, I was able to clearly image blood vessels with relatively low exposure time and LED intensity, but the neurons was out of focus (I lowered the miniscope body as low as possible.. but it seemed that I had to go more low to focus on the neurons expressing GCaMP6f

2. In some mice, the screen was black.. and when I increased the exposure time and LED intensity to the extream, bright spots(looked like neurons expressing GCaMP6f) appeared on the screen(the background was still black and I couldn't see any blood vessels). I thought a sheet of clotted blood on the bottom of GRIN lens might have caused the issue. However, when I sacrificed the mouse, the lens and brain was clean. (maybe the lens was slightly uprooted?)

Has anyone experienced same problems as mine?

TaeHyun

5

Data Analysis / Re: Error message while running msRun

« on: September 06, 2016, 10:55:03 AM »

Hi Daniel,

I was using files in  CA1 Linear track, animal G95 day 10

As you advised, I downloaded different files (Subiculum Open Field) and ran into same error message.

Then, I realized that using only msCam1.avi and behavcam1.avi, settings_and_notes, Thumbs, timestamp.dat filed (since using whole sets of .avi files took so long to analyze..) might have caused the problem.

When I used the whole sets of video files, there was still a message in the beginning:

>> msRun
Problem matching up timestamps for H:\04- 실험 data\Miniscope\Subiculum Open Field-20160903T015036Z\Subiculum Open Field
Calculating column correction. 7.7759% done

but the analysis process smoothly moved on to behavior part.

So.. not using the whole video file set was the problem I guess?

And here is a following question;

Is there any way I can analyze only a subset of recorded video files?

For problem in selecting LED, I had an error message like :
Unknown function hsvthreshold ...
but the error message was gone after I copied hsvthreshold file from util folder to SingleFunctions folder

Thank you for your advise!

TaeHyun

6

Data Analysis / Error message while running msRun

« on: September 02, 2016, 10:09:11 AM »

Hi,

We just began our GRIN lens implantation surgery and I was trying to run the MATLAB data analysis files on your sample images before I get mine.

I was running msRun and I got this error message:

Extracting dF/F traces: 90
Extracting dF/F traces: 100
Reference to non-existent field 'time'.

Error in msExtractFiring (line 9)
V.dt = mode(diff(ms.time))/1000;

Error in msRun (line 52)
ms = msExtractFiring(ms);

When I erase ms = msExtractFiring(ms); in msRun, it goes well but I get another problem selecting LED:

should I just click on LED or drag and draw a circle around LED?

Nothing happens after this

Select ROI
Keep ROI? (Y/N)y
Select LED

even though I selected the LED on Figure 1 pannel..

Has any one experienced same issue?

I have no one with  experience in MATLAB programming and am pretty lost....

Hope you could give me some advice on these matter

Thank you,

 TaeHyun