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zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
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Restrict ROI coordinates misinterpreted after Importing Results #33

Open mcquillr opened 8 years ago

mcquillr commented 8 years ago

I went to look through data I analyzed the other day and after importing a results file and restricting to an ROI I found that the ROI I selected and then one interpreted by ThunderSTORM are not the same. This issue persists even with the latest developer build available through the plugin updater. To reproduce the problem:

  1. Import Results
  2. Draw a box around a cell
  3. Click Restrict to ROI mcquillr.zip
mcquillr commented 8 years ago

I seemed to have stumbled upon a workaround for this issue. Here are the steps you need to take when going back to select cells from previously analyzed data:

  1. When you analyze your data make sure you visualize your results using the Normalized Gaussian method.
  2. In the ThunderSTORM menu select "Import/Export > Import results” and make sure the “Live preview” box is checked.
  3. After you have imported the results, click the “Visualization” button at the bottom.
  4. Manually set the “Left top x [px]”, “Left top y [px]”, “Width [px]” and “Height [px]” boxes to the size of your imaging area (i.e. 0, 0, 100, 100).
  5. Under the “Visualization options” section make sure the “Method” is set to “Normalized Gaussian”
  6. Hit “Ok” and start selecting your ROIs.
cleterrier commented 7 years ago

I also have never managed to get the "Restrict ROI" working after importing localization files.

DavidVirant commented 5 years ago

Has anyone found a solution for this yet? I know it's been a while and Thunderstorm isn't really being maintained anymore, but it would be nice to know if someone in the community figured this out! (mcquillr, that solutions doesn't work for me, for some reason)