Unable to collect binned images
Added by Tom Houweling over 11 years ago
We have configured the K2 dimensions to be 3710 by 3838 for the linear mode in instruments.cfg file and have commented out the counted and super-resolution camera modes.
Using custom camera settings (926x926 with offset 0,0 and bin by 4) we can collect the bright and dark references without any errors. However, when using these camera settings to take an atlas with the gr preset, the images appear to be in counted mode (pixels have only a few values).
Any attempt to collect images that are binned by 2 also failed in the same way (despite new references with the binned by 2 settings collected without error).
Unbinned images are collected correctly in linear mode for the atlas, and using other presets.
Previously binned by 2 images were possible. We may have corrupted something that we cannot trace/overwrite now.
Thank you for any help.
Replies (2)
RE: Unable to collect binned images - Added by Rui Zhang over 11 years ago
Here is an exemplary image that we suspected to be a counting-mode image even though we have disabled the counting and super-resolution modes.
RE: Unable to collect binned images - Added by Anchi Cheng over 11 years ago
To be honest, we have not used binned linear mode at all. Counted mode worked so well that we do all MSI in there. Some users take the final exposure in linear mode.
Have you updated the pyscope on Gatan computer lately? We worked out a few bugs regarding the newer version of DM recently. Most of
them have to do with super resolution mode but it might help you as well.
Please look over our preset design and the modified "Quick Start" instruction that we use for K2 and DE-12.
I spotted three issues from the image you posted.
First, Your image is saturated (min=0, max=65536). Other than getting bright and dark,did you acquired an corrected image while you were in Correction node and or check if the bright and dark images looked normal (bright has more counts than dark). The saturation in that image can come from either that the intensity value saturated the readout (linear mode has very high dark value and is proportional to the exposure time. If your exposure is long, it will not be able to handle well. Second, your custom configuration might not be the same from database point of view so it didn't do any dark gain correction at all.
If the image is from counted mode, DM would have retracted camera by the time it is saturated, so I don't think it is a counted image that you see, more likely an uncorrected linear image that we get from DM/SerialEM plugin as integer.
Second, there is no need to keep the image square. You can use the full camera area.
Third, the image you show covers only one square. This means that you will need hundreds of images to cover the whole grid. You will need to go down in mag for any DD camera because their pixel size are typically 3x smaller than what you were used to.
Fourth, at least on F20, we can use counted mode for gr atlas as well, just needed to be at different spot size.