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Messages - chalspark

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Optics / Re: Calculate magnification
« on: November 29, 2016, 02:03:09 AM »
Hi Daniel,

We used 5mm Dia. x 12.5mm FL, MgF2 Coated, Achromatic Doublet Lens.

Could you tell me formula in order to calculate magnification?


System Assembly Troubleshooting / Re: 3d printing files for the daq board
« on: November 28, 2016, 09:00:24 AM »
Hello Daniel.

We have PCB board of USB_control v2.01.

Which version of case we should buy?


Optics / Calculate magnification
« on: November 28, 2016, 08:44:52 AM »
Dear all,

Hello. Is anyone can calculate magnification? or um per pixel?

we used 1.8mm Dia, 670nm DWL, 0.0mm WD, Uncoated, GRIN Lens. (

In web site, magnification is x6 to x7 and ~1um per pixel.

How can i calculate these value?

It will be help for scale bar into image.


Data Analysis / Re: Calculate spatial firing rate
« on: November 02, 2016, 06:20:17 AM »
Hi Daniel Aharoni,
Thanks for quick reply. Yes. I already have everything to generate spatial firing rate maps, like you said(behav.position and ms.firing). There are few questions to generate rate map.

I got the value of x-position(horizontal) from behav.position(:,1) and calculated occupancy of each bin(histcn/sampling_rate (sec)). In this step, I was expect that sampling rate is 30fps. It wasn't, because maxFramesperFile was 1000. Also, ms.maxFramesperFile was 1000. It means that down sampling 30fps to 20fps.

Q1. Should I use maxFramesperFile to 1000? Why limit maxFramesperFile? Down sampling doesn't matter to calculate occupancy. I am just curious.

I got the firing data from ms.firing(:,segments). When I generate rate map(or place map) with spikes data from single unit recording, spike time was accurate. I find peak point using findpeaks() with threshold. In your paper(Nature,2016), 'Place fields were calculated by deconvolving calcium dF/F traces with an exponential to extract approximate spike times.'

Q2. How do i extract approximate spike time from data? Is one peak of firing one spike?

Finally, I try to run script with all msCam data from G200(behavior data limited 1 to 14). I think data was split because parallel processing. When running msBatchSegment, MATLAB has memory problem. Physical memory was enough when i was monitor memory information.

Q3. How do i solve memory problem?

I'm newbie in optical recording. Sometimes, I asking stupid question. Please forgive me. Your answer will help to generate rate map as you draw. It will be great experience to analyze own data.


Data Analysis / Calculate spatial firing rate
« on: November 01, 2016, 09:22:03 AM »
Hello. I always thanks miniscope for sharing great method for neuroscience.
I tried to analyze sample data(G200) before I get mine. In Github, there are no exist the function of msLineatSFR(it maybe msLinearSFR). I think it was missed or deleted.
May i get the script file for calculating spatial firing rate?

Data Analysis / Re: Error message while running msRun
« on: November 01, 2016, 09:10:51 AM »
Hello TaeHyun,
msRun.m script doesn't include function in order to show dF/F. If you want to check result of dF/F, we should use msRastorPlot function.

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