Appion

I have extended imageloader.py in r19363 to do this. Only thing left is to modify web help string.

One problem I did not solve is the initial guess of tilt axis orientation, called phi in the tomography prediction which is the only prediction value the tomography pipeline cares, I think. It is set to 0 now.

I can upload and protomo2aligner.py done what it can until needing to run. The cluster with protomo2 installed properly is down now so that is as far as I can get.

To test, use the method 1 in upload images (read the batch file). Add at the end tilt angle (degrees, already possible before this), and then dose (electrons per angstroms). Use group images by tilts and set the number of images per group to the number of tilts. The program will figure out the rest.

This is great, thank you Anchi. The tilt axis orientation, phi, must be the tilt azimuth. The user should definitely input this value.

I am not sure where the tilt-series uploader is on myamiweb. Could you point me to it?

Have you ever upload images ?

See Upload_Images_to_a_new_Project_Session

I've only ever uploaded them directly from the microscope. Haha=)

I can upload a tilt-series and with Revision 19365 the tilt-series can be processed through Appion-Protomo.

Should I work on putting places for dose and phi (azimuth) into uploadimage.php or are you working on that?

We only need azimuth. dose part just need modify help.js Go ahead and do it. I have other things to sort out now.

I added azimuth to the webpage (uploadimage.php) and as a parameter in uploadImages.py, but I cannot find in the image tree where I should put record azimuth in the database. This still needs to be done.

Go ahead