spontaneous calcium activity analysis

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Sat, 09/27/2014 - 05:12 am

Hello,
I am a new user of Igor Pro and I would like to ask some questions regarding analysis of spontaneous calcium activity. I have Igor Pro manual, but it is a bit complicated.
I have some questions:
I do not know how can I
1)reduce the amount of noise in the images?
2)calculate deltaF/F?
3)draw a graph ın Igor pro from my values coming from my images to calculate spontaneous calcium activity (like http://www.mediacy.com/index.aspx?page=AS_144)?

4)I learnt how I can make particle analysis (like http://www.wavemetrics.com/products/igorpro/imageprocessing/imageanalys…) and have a table from an example image for calculation in the file-->example analysis-->imaging-->image processing but I can not do same thing when I loaded my image. Why? Image section on the top of the screen is not appearing.

5)I want to select some ROIs myself from the image and have a calculation table from only these ROIs. How can I do that?

If you help me, I would greatly appreciate.

Thank you for your time and consideration.
You need to be a lot more specific in order expect useful answers unless someone on this forum knows exactly what you want to accomplish. Generally an example image or an Igor experiment with some sample data helps.

neuroscientist wrote:
I have some questions:
I do not know how can I
1)reduce the amount of noise in the images?


That will depend on what you mean by noise.

neuroscientist wrote:

2)calculate deltaF/F?


I don't know what that means. I assume you want to write or need a user defined function which takes input to calculate the desired value(s).

neuroscientist wrote:

3)draw a graph ın Igor pro from my values coming from my images to calculate spontaneous calcium activity (like http://www.mediacy.com/index.aspx?page=AS_144)?


The problem with such a link is that people need to read through and try to filter out what might be important for you...only a few will do that. Or are you just asking how to do a X-Y plot?

neuroscientist wrote:

4)I learnt how I can make particle analysis (like http://www.wavemetrics.com/products/igorpro/imageprocessing/imageanalys…) and have a table from an example image for calculation in the file-->example analysis-->imaging-->image processing but I can not do same thing when I loaded my image. Why? Image section on the top of the screen is not appearing.


Without more details what exactly you have done it is difficult to answer. Maybe you just need to display the image first.

neuroscientist wrote:

5)I want to select some ROIs myself from the image and have a calculation table from only these ROIs. How can I do that?


Most (or all?) image analysis operations take an /R flag and a ROI mask. Another way is to work on a copy of the image using the Duplicate /R=(startX,endX )(startY, endY ) command to only work on a part of the image.

neuroscientist wrote:

I have Igor Pro manual, but it is a bit complicated.


The manual can be quite overwhelming but it's very concise with lots of examples. If you can break down your task into simple steps (image import, display, particle analysis, etc) it's a lot easier to help specifically and to find the right sections of the manual. Definitely make sure you read carefully sections I-1 and I-2 of the manual.

September 28, 2014 at 10:27 am - Permalink

neuroscientist wrote:
4)I learnt how I can make particle analysis (like http://www.wavemetrics.com/products/igorpro/imageprocessing/imageanalysi...) and have a table from an example image for calculation in the file-->example analysis-->imaging-->image processing but I can not do same thing when I loaded my image. Why? Image section on the top of the screen is not appearing.


I suspect your image was loaded as an RGB image instead of a false-color (grayscale) image.

Either change the way you load the image, or convert it from RGB to gray using

Imagetransform convert2gray nameOfRGBwave

ImageTransform convert2gray converts an arbitrary 2D wave into an 8-bit normalized 2D wave. The default output wave name is M_Image2Gray.

--Jim Prouty
Software Engineer, WaveMetrics, Inc.

September 28, 2014 at 01:42 pm - Permalink