Leginon

Could you give me a screen shot of your upload image settings before you have it run ? It appears that you've got it half way but not all the way.

Image upload runs in two basic modes:
1. uploading all images in the same folder of a particular type. All images should have the same pixel size and one nominal defocus is entered.
2. uploading path specific images with individualized values. The specification is in the batch file that you entered.

The website you posted is a private site. System administrators at each myamiweb server decide who has what permission to do a task. You will have to ask those who managing that to set up the permission.

Thanks Anchi,

I haven't been able to access the system this week to do the screen shot (the only Linux computer we have is in a different building etc etc!) but this is what I did;

I went in to the project database, added new project then 'upload new images to session'

I put just one tiff image in the Appion home/Images folder.

On the Upload Image page;

Images grouped by: none
Session name: 16feb17z (I presume this is automatically selected)
Session description: test1
Scope Cs value: 2 (I don't actually have the Cs value for our microscope - is it critical?, even the engineer who was in to service the microscope didn't know it!)

2.Enter parameters manually

Directory containing images: Appion Home/Images (I wasn't sure how to enter the path....)
File format: tiff
Pixel size (A): (is the A angstroms?)
Binning in x: 0
Binning in y: 0
magnification: 80 000
high tension: 75
defocus: -1.5

I presume I couldn't upload because I didn't have all the information about the image......

Can I also ask - is the appion processing strictly for cryo-EM only or can it be used for negatively stained TEM images?

Thanks again,

Sonya

Hi, Sonya,

For low high tension negative stain work that does not go to near atomic resolution, Accurate Cs value is not critical. You can put 2.0 mm.

Directory containing the image: Use absolute path. Remember that the web server needs to have access to the directory it is uploading. This is not like uploading your photo to the cloud. It is just a copy of the files to organized location and record its location and information in Appion/Leginon database so that it can keep track.

Pixel Size: Yes, A meant to be Angstroms

Binnings: No binning is 1, not 0

The rest is good.

Appion is used for both negatively stained images and cryo-EM.

Thanks Anchi, v helpful. Will give it another go next week.

Ok I'm getting somewhere but still not completely there!

I tried to upload a tif file from our TEM but got the error message 'image conversion to mrc did not execute properly (please see screenshot4)

I also tried to open an mrc file which I downloaded from https://login.nanoimagingservices.com/myamiweb/imageviewer.php?expId=7382 - we have permission to copy/download files.
This seemed to execute but when I opened the test in the Image viewer I got a 'Failed' message (see screenshot3 and screenshot2 and screenshot2a)

I also tried saving the mrc file as a tif and then uploading it but got the same error message as with the tif from our TEM

Any advice?

Thanks
Sonya

The tiff file did not read properly. EMAN is used to do that. As tiff files can be very broadly defined with color and other information, em softwares may only read one kind. If you can convert first to mrc, it should work. By the way, filenames with spaces may cause problems later on. I recommend replacing them with _.

The mrc file upload appears to be successful. The error about "Redux does not return anything" may be problem of the image server, redux, Are you sure it is on ? You can check the test image page described in Using Redux to serve images on myamiweb under the heading of Test the myamiweb and Redux installation

If that is successful, then it means that the apache user which the webservice starts on has no permission to read the file at where the upload goes.