Hi Stav,
I think there might be a simple fix: you can use the -byte 0 option to force newstack to write unsigned 8bit number in mode 0 files:
newstack -by 0 t2.mrc byte.mrc
Because the counts should all be small positive numbers, forcing writing unsigned number should has the same effect as writing signed, but not shifted int8 into the mode 0 MRC. (If there are spurious negative numbers, damaging them by forcing poisitivity should not cause much negative effect anyways.)
My test with the small chunk of mode 0 file you sent me seems to have worked : all 0x80 are now 0x00 and 0x81 now 0x01. I do not have 4-bit MRC file so Please try it and let us know.
Zhijie
Some updates after Stav shared a chunk of mode 101 file (thanks, Stav!) :
In the mode 101 file, most pixels have readings of 0, 1 and 2. This is consistent with the serialEM description that when saving in mode 101 the range of counts is 0-15. In other words, the 4-bit integers are unsigned.
K2 super-resolution or K3 unbinned counting mode images are stored with pairs of 4-bit integers (maximum 15) in each byte. (The left pixel in a pair is in the low 4 bits and the right pixel is in the high 4 bits of a packed byte.)
This simplifies the reading of the mode 101 MRC files a lot (as opposed to, if the 4-bit int are signed): we can simply &0x0f to get the left pixel and >>4 to get the right pixel from each byte.
Zhijie