Template picker did not pick the whole image

Particle Picking
1

Hi there,
When I used the Template Picker in V2.13.2. It successfully picked all the micrographs, but not the whole area of each micrograph. Even when I used the inspection tools, it still showed not the whole image getting picked. For the auto-picking, expect the diameter, all the other parameters were set as default.

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image1428×1018 347 KB

Does anyone come across similar problems?
what was worse is that most of the images are not picked (10k particles out of 10k micrographs!!)
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image1194×319 77.9 KB

Thank you so much.
Tinghai

2

I seem to see this, except the image is also not displayed properly. Maybe this is just a display issue? We’ll see if my particles are extracted properly.

image
image594×605 23.4 KB

3

I’m experiencing the same issue as Daniel.

Import of micrographs, GCTF, CTFFind, and Patch CTF all seem to function properly (according to the outputs and pngs).

Particle picking seems to occur against a greyed image (certain features of the image are discernible under careful scrutiny, such as the edge of the hole).

4

More notes.

Particles are actually centered on something:

image
image1022×222 59.5 KB

Is it related to the minimum distance from the (top and right) edges of the image?

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image753×534 320 KB

5

In the auto-picking job, I see the same thing, not displayed correctly. In the inspection job, I see the above images. I tried the RELION CPU motion corrected K3 micrographs, or motioncorr2 corrected K3 micrographs, they all look the same.

6

Example of A) the original micrograph, B) the flat grey image displayed during picking, and C) a quick photoshop to highlight discernible features (note the contamination on bottom left and carbon on the right.) As Daniel suggested, there seems to be an issue with contrast in the displayed image. Additionally, the displayed image crops out portions (most notably on the right) of the original micrograph.

comparision
comparision1016×2154 1.48 MB

7

Hi @PeterXTH @DanielAsarnow @sergei.pourmal
Sorry about this issue - it was noted already and has been fixed but has not been deployed yet. It only occurs for imported K3 micrographs that were motion corrected outside cryoSPARC - it does not happen if you import movies and perform motion correction in cryoSPARC. For now you’ll have to roll back to v2.12 until we deploy v2.14, or import the raw movies.

See:


8

Hi @PeterXTH @DanielAsarnow @sergei.pourmal

This has been fixed and released in cryoSPARC v2.14.0, out now! Thanks for reporting.

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