Report From User on 7/11/19

[grantnikseresht]

1. Right now the image summer can only sum sequential images, but it would be really helpful if it could phase average, as in sum every 20 images for example. It would also be great if it could take a series of images, and a user could input a .csv file of some kind and the program would sum images in custom groups. One thing we do is take diffraction images of tethered insects in flight while recording wing strokes with a high speed camera to get length and phase of the muscle. So when we want to phase average those we won't be able to just sum every n images, we will need to sum user defined groupings since the diffraction images won't be phase locked.

2. I have tried to make my own image summer in Matlab and can open my summed images in ImageJ, but can't open them in MuscleX. Can you let me know what parameters/settings have to be set so that I get my summed images to work with MuscleX? I am particularly interested in getting this working for me so I can go ahead an start phase average without waiting for the next version of MuscleX. I believe its just a problem of setting the right parameters. I have attached my Matlab code and in case its helpful for you to look at.

3. Can you let me know if there is anything different I need to do to get MuscleX to work with the Eiger and the MarCCD? I haven't tried to use MuscleX on them yet. I also would need to sum those images, is there anything I would need to do differently regarding setting parameters to sum those, re: my second question?

4. All the images I have done so far have been from the Pilatus, and it seems like MuscleX quite frequently has difficulty finding the center of the image. Is this because of the black bars from blank pixels in the Pilatus?

5. Right now to find the equator in a series of images, it seems MuscleX can either do fixed angle or can guess it's own angle. But sometimes neither are ideal, for example if there is metal flare during periodic contractions, MuscleX will align to the metal flare, but since the muscle is oscillating the equator axis is changing too, so neither the fixed angle or max intensity work great and then a user has to manually fix the angle for every image. It would be helpful maybe if a user could specify an average angle for the whole series and then MuscleX could find the best alignment within +/- x degrees for each individual image which should solve that problem.