Upload K2 movies as movies into Appion
Added by Michael Cianfrocco almost 9 years ago
Hello,
Is it possible to upload movies into Appion as 'movies', instead of Appion summing the images and then uploading the individual image? When providing Appion with the movie stack, it sums the movie and then uploads the individual image.
Or is it that movies have to be input into Appion directly from Leginon?
Thank you for your help!
Mike
Replies (1)
RE: Upload K2 movies as movies into Appion - Added by Anchi Cheng almost 9 years ago
See how to use this feature at http://emg.nysbc.org/issues/2801
What the upload does is to organize the files, putting the movies in /your_data_storage/frames/your_upload_session and the sum image in /your_data_storage/leginon/your_upload_session and then record in the database as such. Later on, it will know that the image has a movie associates with the sum and where to find it and therefore behaves the same as a Leginon collected data set.
It is done this way because, if you are uploading movies, it is likely because you want to process it in appion for particle picking etc., and most initial processing requires a sum image otherwise they need to do the summing at each time, that is too tim-comsuming.
If you are loading raw movies that needs flat field correction (and maybe dark correction for DE camera), you should also supply it during this upload (see the above link for how to specify it). This way, it can apply it in the summing and the frame processing can do flat field correction on individual frames for you.