I am just following the T20S tutorial. I reconstructed the structure pretty well. However, I just want to know how to extract the particles to individual files e.g. .png/.tif.
(1) I did manual picking followed by template picking
(2) YES, I can inspect picks before extracting them. The images shown in cryoSPARC before and after extracting are both quite good.
(3) YES, I can run 2D classification and finally do ab initio reconstruction and refinement of T20S correctly.
Everything is good, and I can perform the 3D reconstruction correctly.
However, when I examine the .mrc images generated at each step (e.g. patch motion correction, particle picking, extract of particles), I can not observe any particle in these noising images (only the class average is recognizable). I use imageJ or python codes to open these image stacks and convert them into image. Have you done some filtering to make the particle visible as shown in cryoSPARC?
All in all, the images shown in UI and preserved in the folder are not quite the same:
Original image and the image shown in the webapp :
The image in the folder of the job “Patch motion correction”.mrc