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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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Scipion monitor - monitoring actual defocus - feature request #915

Open JuhaHuiskonen opened 7 years ago

JuhaHuiskonen commented 7 years ago

In some data collection schemes, more than one acquisition areas (for example 4) are defined for each hole and each area has a defined target defocus value (for example 1, 1.5, 2, 2.5 microns). In such cases it would be useful if the defocus monitor could plot the distribution (as a box plot) of the estimated defocus values for each of the areas separately. (If there is only one area per hole, this would still be useful, as it would plot the range of estimated defocus values.)

delarosatrevin commented 7 years ago

Hi @JuhaHuiskonen, thanks for the suggestion. Do you have some example of this plot that you have done manually? So we could have a better idea of what are you suggesting. I there any way to relate the movie filename with the area (and nominal defocus)? Remember that the import from Scipion only checks in a given folder and has no communication with the acquisition software. I think there are some xml files from EPU that contains some metadata per movie...and not sure if we are storing this information now. We were discussing about that some time ago for other purposes.

azazellochg commented 7 years ago

Hi all, I think here is a not bad example of Focus software https://status.c-cina.unibas.ch/status.php (just increase time range to see the data). Can be used as an idea for future monitor/scipion box improvements

delarosatrevin commented 7 years ago

Thanks @azazellochg , I agree that there are some nice plots that we could incorporate in the future.