High resolution image of 2D classification

2D Classification
15

I have two alternative solutions.

Solution 1:
I don’t know if I’d call it simple, but… I use EMAN2 to display images. EMAN was one of the original 3D reconstruction tools. I don’t use it for that anymore, but still find it to have a very useful set of tools. I can run it from my Mac, so that’s handy too.

  1. Install EMAN2: https://blake.bcm.edu/emanwiki/EMAN2/Install
  2. Go to the cryoSPARC project folder and the job folder for the 2D class averages you want. You should see a file that looks like this: cryospac_P##_J##_020_class_averages.mrc. That’s the file you need to display. Download or copy that file to your local computer (or wherever you installed EMAN2).
  3. Run this EMAN command: e2proc3d.py inputFile.mrc outputFile.mrcs. This converts the file from .mrc (which will be understood as a 3D volume) to a .mrcs (which will be understood as a stack of 2D images.
  4. Then to display the image, run this command: e2display.py outFile.mrcs.
  5. When the image displays, you can middle click to get a popup window that allows you to adjust the magnfication, which you should set to 1, and the brightness, contrast, and gamma, which you can adjust how you like to make the averages look pretty. You can resize the image window to make it however many column/rows you want it to be.
  6. The crazy part, is that you then need to take a screen shot of that image. That’s the only way to save. But if the magnification = 1, then everything is ok, and the image will have the same number of pixels as the actual reconstruction.

Solution 2:

  1. Install Fiji: https://imagej.net/Fiji/Downloads. Fiji is just a version of ImageJ with the necessary plugins already added. The advantage is that it’s a point and click installation and usage. It will open mrc files automatically. You can save them in any format you like. The disadvantage is that it opens them as a stack, so you get one class average at a time. If want to tile them, the way you normally view 2D class averages, you will have to tile them yourself in some other program.

Best,
RJ

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