Alignment of two colour maps

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Michael Shannon

Jun 25, 2016, 9:14:31 AM6/25/16
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Hey all

So we have some reliable two colour STORM data - just wondering whether thunderSTORM has a way to easily align (using fiducials) and colorise the two maps.

If not, can I use it to in some way get around the problem (by concatenating and doing a fiducial based drift correction, and then somehow unconcatenating again)?

Thirdly, if thunderSTORM is not recommended for this - is there somewhere i can go that will accept CSVs like this and allow two channel alignment/visualisation?

Thanks everyone,

Mike Shannon (Dylan Owen lab, KCL)

Sep 12, 2016, 9:44:09 AM9/12/16
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Well if the two colors have been recorded right after each other you could just append the 2nd color to the first list, offset the frame number and run the drift correction. This can be even done in programs like Excel.

If there is a time gap you would need to calculate the corresponding frame for the events of the 2nd color.

If you are familiar with MATLAB or something similar - you can work on the raw localizations to align them. I use this built-in function: which gives me good results (even without fiducials - depending on your structure of course)

For 2-color-visualization I either use FIJI and just load the two separate super-resolution images (after the aforementioned drift correction) - combine them into a stack and assign the colors to them. Or I just use a standard image editing software (like photoshop, gimp, ...). I find it too cumbersome to do that in MATLAB and fiddle around in the RGB space.

Philip Gröger (BCUBE, Dresden)
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May 27, 2018, 12:25:35 PM5/27/18
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Is there any way to use a beadmap to overlay two channels in THUNDERSTORM ImageJ program itself?

I usually image my two-color images first 647 followed by 532 and then have a seperate tetraspec beadmap image taken in both channel which I want to use for two color-overlay.

I did not find any specfic information in the manual.


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