Hi,
No. The values of individual pixels.
If the conversion failed (e.g. type error),
the values will be clearly strange (all zero, all one,
all large numbers, etc).
The true gain should be floating point numbers close to one.
Best regards,
Takanori Nakane
On 2019/08/11 9:24, Yehuda Halfon wrote:
> Do you mean the Pixel spacing (Angstroms):
>
> For both of them its:
>
> Pixel spacing (Angstroms).............. 2.675 2.675 2.675
>
> ------------------------------------------------------------------------
> *From:* Takanori Nakane <[log in to unmask]>
> *Sent:* Sunday, August 11, 2019 11:19:45 AM
> *To:* Yehuda Halfon <[log in to unmask]>; [log in to unmask]
> <[log in to unmask]>
> *Subject:* Re: [ccpem] The new embedded K3 in EPU gain reference file
> Hi,
>
> You should look at the actual pixel values.
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/08/11 9:17, Yehuda Halfon wrote:
>> Hi all,
>>
>>
>> I took the dm4 file from GMS and converted it to MRC the header is the
>> same except for this 3 lines:
>>
>> In the DM4:
>>
>> Minimum density ....................... 0.0000
>> Maximum density ....................... 0.0000
>> Mean density .......................... 0.0000
>>
>> In the MRC:
>> Minimum density ....................... 0.52489
>> Maximum density ....................... 1.8188
>> Mean density .......................... 0.99965
>>
>> In the MRC from Serial EM it looks like this:
>> Minimum density ....................... 0.10000E+38
>> Maximum density ....................... -0.10000E+38
>> Mean density .......................... 0.0000
>>
>> Do you think it will make a difference?
>> Or should I use other option from dm2mrc?
>>
>> Yehuda
>>
>> ------------------------------------------------------------------------
>> *From:* Collaborative Computational Project in Electron cryo-Microscopy
>> <[log in to unmask]> on behalf of Wim Hagen
>> <[log in to unmask]>
>> *Sent:* Thursday, August 8, 2019 4:18:56 PM
>> *To:* [log in to unmask] <[log in to unmask]>
>> *Subject:* Re: [ccpem] The new embedded K3 in EPU gain reference file
>> Hi
>>
>>> On 8. Aug 2019, at 14:53, Takanori Nakane <[log in to unmask]> wrote:
>>>
>>>> Counting gain reference = 1/(bin(1/Superres gain reference))
>>>
>>> Thanks. This makes sense.
>>> "bin" means adding 2x2 pixels in the real space, is this right?
>>
>> Yes, that’s correct.
>>
>>> Hi Yehuda,
>>>
>>>> I'll ask our TF guy, and we'll try to use the gain from GMS, its dm4 so
>>> we'll need
>>> to convert it to mrc.
>>>
>>> You can use 'dm2mrc' from IMOD.
>>
>> Keep in mind that the images can have a rotation, but the gain ref is
>> always written in native orientation, so no rotation or flip. I've also
>> experienced issues with tif handling, in some cases one needs to flip
>> the gain ref in Y, to my knowledge IMOD dm2mrc does already do that, so:
>> - SerialEM tif and an IMOD dm2mrc generated gainref.mrc works in Relion.
>> - SerialEM tif in Warp or cryoSPARC requires flip Y on gainref.dm4 .
>>
>> No idea what tif format EPU gives, but writing a different size gainref
>> sounds like a clear bug to me.
>>
>> Best,
>>
>> Wim
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