Leginon

Is the tif file an mrc stack ? The error suggests that the conversion made it into a 3D mrc.

The tif Files should just be 2D images, but the upload did try to convert them to mrc files.
I tried uploading 50 different .tifs and when I look at the project which holds the files, there are 50 different uploaded files that all show that error, so I don't think it tried to combined them into a 3D image.

dm3 format upload was written quite a few years ago. There might be change in the format that the library used is not doing right. Can you give us the camera, Lattitude and GMS version where it is produced from ? I can use that to ask Gatan.

If you can make a small tif file that does not convert correctly and attach here or create an Issue on redmine, I can ask others to look into solutions.

Thanks.

Anchi

I will follow up with information on the camera at a later point, but in the meantime, I will attach one of my tif files here. Does it effect things that I made these tifs by converting .jpgs?

Thanks,

I want to check the header with this, so converted by another program is not good. Please send me a file from the same program as the ones you try to upload. Thanks

The file I sent is one of the ones that I tried to upload.
I converted them by changing the extension because Appion will not upload .jpgs

As far as the questions you asked previously:
As answered by my facility manager:
"Our camera is a Gatan UltraScan 1000. Our camera software is Gatan Digital Micrograph 2.12. It predates when Gata started calling it GMS (Gatan Microscopy Suite). I am not sure what Lattitude is? Do you mean exposure latitude? If so, I gain normalize our camera at 4000 counts per pixel per second."

Let me know if you need anything else,

Hello,
Is there anything more on this front? Anything that I should do to try to get this working for me?

Sorry for the delay. I just opened the file you sent now and that reveals a big problem. images we want to upload is in general represents only pixel values from the camera. Therefore, they would be a grey scale image without any other color nor scale bar. That is not so of your tiff image. I would not recommend trying upload something like this.

Ok, so you think that that would solve the whole issue if I were to use images that were only grey-scaled?
Is it the same problem with my .dm3 files? Or is there a different problem here?

Is my problem with the dm3 files the same? Is the EMAN failing because my dm3 files contain color? If not, what can I do to try to fix this?

I believe EMAN1.9 is being used to convert anything that is not an mrc or tif formatted file. Can you try running the command:
proc2d <input file> out.mrc edgenorm flip mrc
with one of your dm3 files and let us know if it converts properly? You can check that it converted by using an MRC viewer (e.g. boxer from EMAN)

It's telling me that there is no such command as proc2d

I see. That's the issue then - your options are to install EMAN 1.9 on the machine that is performing the upload, or find a program that can batch convert your files to mrc & upload those instead so that it bypasses the EMAN 1.9 requirement.

When my IT guy tried doing the whole appion install, he sent me this:

"It looks like the Appion autoinstaller didn't install EMAN, and the instructions for installing EMAN seem to not work correctly on CentOS 7."

Do you know a better, reliable way to intall EMAN?

I've never had to install EMAN, this has always been taken care of by the IT folks. EMAN2 may be an option since it's udpated, then you could use that to manually convert your dm3 files to mrc for upload.