Messages

211

Electronics / Re: Coax communication frequency

« on: August 18, 2016, 11:32:12 PM »

All the communication and data transmission will be below 3GHz. One other thing to be concerned with when looking into commutators is their impedance. Ideally you want a 50Ohm impedance commutator. If you cannot find one of those, make sure any non-coaxial cabling is as short as possible and that the wiring inside the commutator is relatively short.

We have been using commutators from DragonFly with great success. Their commutators are not specs for 50Ohm impedance but they still work great as long as we keep any non-coaxial cabling as short as possible.

212

Data Analysis / Re: Error in msExtractFiring and additional basic questions for analysis

« on: August 18, 2016, 11:28:03 PM »

Hi Jesper,
msExtractFiring() implements an algorithm developed by Vogelstein, http://www.stat.columbia.edu/~liam/research/pubs/vogelstein-fast.pdf. His source code, Fast_Oopsi can be found on GitHub here, https://github.com/jovo/fast-oopsi. I don't think I have run into this particular error in the past but I will try to see if I can reproduce it. msExtractFiring() attempts to deconvolve out the slow calcium decay from the dF/F signal. Fast_Oopsi is a particularly good approach to doing this but you can also work with some more straightforward deconvolutions such as the deconvlucy() function in MATLAB.

Answers to your other quections:

• The output of msSelectFluorThresh(), ms.goodFrames, is currently not implemented in the analysis code on GitHub and therefore the threshold selected has no affect on the rest of the analysis. I left msSelectFluorThresh() in the main workflow so people could quickly take a look at how fluorescence changed across each recording session. As for the ROI selection in msSelectROIs(), we usually select an ROI about 1/8th the area of the entire frame. The ROI should avoid the edges of the frame and should contain a landmark (blood vessel or cell that is constantly visible). msSelectAlignment will display a histogram and meanFrame for each alignment ROI you previously selected. The best alignment will be the one with the least blurry meanFrame and has a clean, localized oval in the histogram.
• After running through the analysis, open up he 'ms' data structure to see what all is stored. dF/F traces are stored in ms.trace, deconvolved activity are stored in ms.firing. The order of the variable in 'ms' are in the same order as how you run the whole analysis.
• The script I use to generate these videos is on my other computer. I will upload it to the GitHub repository later today. For the mean time you can take a look at msPlayVidObj() to display your analysis.

213

Optics / Re: GRIN lense acquisition

« on: August 18, 2016, 12:16:42 AM »

All add a few points to Asr's post.

• Edmund Optics lenses are actually rebranded Grintech lenses. They work well but if all you ever want is a 1.8mm diameter lens. We are working with GoFoton to make an assortment of lenses with different diameters and properties to cover all Miniscope applications. Also, there has been a history of Inscopix/Grintech blocking the supply of lenses to Miniscope users so we do not want to be dependent on these rebranded Grintech lenses.
• As Asr said, most commercial GRIN lenses were not designed of short working distance imaging and therefore produce low contrast/high scattered images. You can check out our wiki page discussing this, http://miniscope.org/index.php?title=GRIN_Lens_Information. I will be updating this page with new information on the GoFoton lenses soon.
• Imaging GRIN lenses need to have a gradiant profile that is a bit harder to manufacture than standard collimating GRIN lenses. We also want to have GRIN lenses that are bio-compatible and an NA of at least 0.5.

214

Electronics / Re: Coax communication frequency

« on: August 18, 2016, 12:07:29 AM »

Hi Honi,
There are 2 frequency bands being sent simultaneously over coax. One sits around 1MHz and handles the back communication such as I2C. The other is on the order of a few hundred MHz and handles data transmission. If you need exact frequency values let me know and I will calculate them.

The hardware is capable of supporting up to 1.4Gbps.

215

Electronics / Re: PCB questions

« on: August 18, 2016, 12:04:44 AM »

Hi Honi,
1) The BOM is on our GitHub Repository under the "Assembly" folder.
2) You can look at the PDF in the v3.0 and v3.2 folder to compare their circuit and layout. v3.2 has a few other added features including mounting holes and an option to mount a MOSFET on the bottom of the PCB to toggle the LED power.

216

DAQ Software/Firmware / Re: Modifying DAQ Software Code

« on: August 12, 2016, 03:26:58 AM »

Hi Cameron,
You should download Visual Studio Community from dreamspark.com (it is a free Microsoft development environment). Also you will likely need OpenCV. Then grab the latest version of the Miniscope source code and project/solution file from our GitHub Repo (I will update the Repo sometime next week). You should then be able to open the project, edit, and compile the software.

217

Electronics / Re: Flickering excitation LED with longer coax cable

« on: August 12, 2016, 03:24:37 AM »

Hi Jesper,
If using the coax cable from Cooner Wire (or something similar) you should be able to run up to (and likely well over) 10' without issue. The source of the flickering LED is likely one of the following;

• Most likely, as MikerVee said, the LED is damaged and needs to be replaced. Once the silicone lens/protector is removed from the LED it can be damaged by direct contact with the light emitting surface when inserting it into the Miniscope body.
• The coax cable has been damaged or has a kink in it that causes a poor connection sometimes.
• The coax cable connectors (possibly the coax cable soldered onto the DAQ PCB) has an issue. You can try redoing the soldering of these connectors.
• If you have version 3.2 of the CMOS PCB, make sure the 2 hald circles on the bottom of the PCB are shorted together with solder.
• Try a different computer. At higher LED power, the LED draws a decent amount of current. It is possible that your computer/USB port is not outputting enough current. This is unlikely.

218

DAQ Software/Firmware / Re: Issues Uploading Firmware

« on: August 08, 2016, 07:57:39 PM »

Excellent! Thanks for the update.

219

DAQ Software/Firmware / Re: Issues Uploading Firmware

« on: August 08, 2016, 04:59:25 PM »

Hi Atkca,
Unfortunately I have never experienced the issue you are having. I Cypress recently updated their software/drivers and now the un-programmed Miniscope DAQ PCB does indeed show up as "Cypress FX3 USB Bootloader Device" instead of "Cypress USB Bootloader." Below are a few suggestions:

• Double check that the switches and jumpers are in the correct configuration on the DAQ PCB (http://miniscope.org/index.php?title=Software_and_Firmware_Setup). If you post a picture of your PCB on this thread I can also double check that everything looks correct.
• Make sure you are using a reasonably high quality, not super long, USB cable.
• Try using a different computer to flash the firmware onto the DAQ PCB.

If you Google "Cypress Boot Programmer Device not found" there are a couple Cypress Forum posts about it (Cypress does a really good job responding to questions on their forum). For example, http://www.cypress.com/forum/usb-30-super-speed/cypress-boot-programmer-device-not-found.

Please keep me updated!

220

Group Miniscope Orders / July/August Group PCB Order

« on: July 28, 2016, 04:51:29 PM »

Hello Everyone, I just setup a signup sheet for our 6th Miniscope Group PCB Order. Ordering as a group decreases per board costs which is significant when ordering only a few PCBs. Expect the DAQ PCB to run about $200 a board and the CMOS Imaging Sensor PCB to run about $115 a board. The company making the PCBs in located in California but can ship internationally.

If you are interested please add your information here: https://docs.google.com/spreadsheets/d/1eXogU7JdeuhMHnVIJBHvCVjgZ6e9KnxPGWvJEBK-eyw/edit?usp=sharing

221

Optics / Re: GRIN lense acquisition

« on: July 26, 2016, 03:20:03 AM »

Hi Austin,
We are currently working with GoFoton to develop high quality GRIN imaging lenses and have made great progress. I think they should have a line of GRIN imaging lenses commercially available within the next couple months.

In the mean time, you can purchase 0.25 pitch, 1.8mm diameter GRIN lenses through http://www.edmundoptics.com/optics/optical-lenses/aspheric-lenses/gradient-index-grin-rod-lenses/3145/#f=categories_s|*C11I*,productId_i|3145,27614_s|1.8. We have sucessfully used part number #64-519 but likely almost all their their 1.8mm diameter GRIN lenses are compatible with our system. For thinner relay lenses, try and contact Inscopix. Most labs have been unsuccessful requesting price quotes from them but a few labs have managed to get them to supply lenses. I think their new stance is they are willing to supply non-Inscopix labs with lenses at a slight markup over their normal customers.

The Doric system uses GRIN lenses from GoFoton but I do not know enough about the specs of their lenses to be able to tell you if they will work in our system.

222

DAQ Software/Firmware / Re: Two LEDS (no DataLink), CMOS LED and LED PCB on, msCam retrieval error.

« on: July 21, 2016, 05:39:54 PM »

Hi Austin,
Glad to hear you are making progress getting your system up and running. With all 3 green LEDs on and stable your soldering job is likely fine. I have a few suggestions for you now:

• Make sure you are connecting the DAQ PCB to a USB3.0 (USB Super Speed) port on your computer. Make sure your USB drivers are also up-to-date.
• Try connecting the system to a different PC to see if the system will connect
• For some reason some PCs require you to click the 'connect' button in the DAQ software multiple times for the software to connect properly to the hardware so try clicking the button a few times.

. 
Please update this post with your progress.