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- In the main menu, click Advanced
- Select Python Console
Go to the File/Open... menu of the Python Console and open the following script: drift_ChangeLocs_Region (2).py. The script file is on the desktop of the Nanoimager PC.
Info If you want to use it on your own copy of NimOS then email lmcb-lm-help@ucl.ac.uk and we will send you a copy.
- User editable values in the script are highlighted in cyan.
- The most important value to adjust is dc.MinPointsPerSubsample. The default value for this when you use the Calculate Drift Correction button is 400000. The text in the script recommends setting this to 5000 or less. I have had more luck with around 10000 with my specimens, but it depends on how many localisations you have.
- You can also restrict calculation of drift to an ROI (if most of your image has no localisations, for example). This is done by changing the dc.CustomRegionLeft, dc.CustomRegionRight, dc.CustomRegionTop and dc.CustomRegionBottom values. The values have to be typed in, so you will have to hover your cursor over the image to get the coordinates.
- I'm not recommending that the dc.MaxSubsampleImageDimension is edited at this time.
- Once you've changed the values to the ones you want, click Run code.
- The image below shows a zoomed up image of two fluorescent labels about 100 nm apart in a DNA origami structure. The image on the left has drift and the image on the right is corrected.
- If the drift correction hasn't worked well, try decreasing or increasing the dc.MinPointsPerSubsample.
- You can use the Apply correction tick-box in the main GUI to toggle the correction on and off.
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