SerialEM-generated defect file format not recognized


I am trying to import movies from a Krios SerialEM data collection run, and the defect.txt file is not recognized by the movie import job. Here is the defect file I have been trying to use:

The error message I get when importing the job says "defect file is in an unrecognized format.

I have already tried using the clip command ini mod to convert the .txt file to a defect_map.mrc as is suggested elsewhere on the internet. The commands I’ve used are:

clip defect -D defects…txt fileWithFrames defects…mrc


clip defect -D defects…txt -f tif fileWithFrames defects…tif

So, I have two questions:

  1. will the cryoSPARC pipeline recognize and disregard dead pixel columns without the addition of a defect file?


  1. If not, how can I convert my defect file into something that can be read by cryoSPARC?

Thanks in advance,


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Hi @ggonza,

Any pixels which have a value of zero in the gain reference will be treated as dead pixels. So yes, defects can be specified without an additional defect file, as long as those pixels in the gain reference is set to zero.

That having been said, we are interested in adding SerialEM defect file support to CryoSPARC. Are you able to make the full defect file (as output by SerialEM) available to us? It would be quite helpful in testing.


Here’s a text copy of one:

CameraSizeX 11520
CameraSizeY 8184
RotationAndFlip 0
WasScaled 1
K2Type 1
FalconType 0
NumToAvgSuperRes 0
UsableArea 0 -1 8184 11519
BadRows 0 1 2 3 4 5 8176 8177 8178 8179 8180 8181 8182 8183

On the K3 the defect file usually specifies only several rows along the top and bottom of the sensor.

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