[Chimera-users] How to change 32bit map into 16bit map

[Jun Ha Song]

Tom,

Thank you for your swift reply! :)

Best,
Junha.

On Thu, Apr 5, 2018 at 4:18 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Junha,
>
>   You use the “vop scale” command to scale and convert a 32-bit float map
> to 16-bit integer.  The reason you get just 4 spikes in the histogram of a
> converted map is because the floating point values ranged say from 0 - 3.5
> and when converted to integer those get rounded to 0,1,2,3.  In order to
> use the full 16-bit integer range (+/-  32000) you’d want to scale the
> float values.  The scale factor you need depends on the range of data
> values (which is shown in the Volume Viewer dialog below the histogram).
> So for example if the floating point range of values was 0 to 3.5 I could
> use
>
> vop scale #1 factor -8000 value int16
>
> If you want to convert to an unsigned integer type (uint16) then you need
> to scale and shift the float values to put them in the range 0-65355,
> values out of range (e.g. negative) will be clamped (e.g. to 0).
>
> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale
>
> Tom
>
>
> On Apr 5, 2018, at 3:50 PM, Jun Ha Song wrote:
>
> Hello,
>
> I sometimes invert my map using Fiji, and I also convert my 32bit map into
> 16bit map using Fiji's "Image →  Type  → 16-bit" function, but the only
> way to retrieve the map from Fiji is to save the map as .tif stack, then
> use IMOD's "tif2mrc" to get it back as .mrc file.
>
> However, once I save my map as .tif, the pixel spacing information of the
> map is set to 1,1,1. Because of this, I always have to re-adjust the pixel
> spacing back to original using IMOD's "alterheader" once I use Fiji for any
> kind of image adjustment.
>
> I know I can invert a map in Chimera (without setting the pixel spacing to
> 1,1,1 like Fiji) by using "Volume Filter  → Filter Type : Scale  → Scale
> by -1", but I don't know how to turn my 32bit map into 16bit map.
>
> Although the "Value Type" of scale filter allows me to specify which bit I
> want the map to be in, when I filter my float32 map with value type set to
> either int16 or uint16, the filtered map shows histogram with only few
> lines.
>
> Can UCSF Chimera turn float32bit map into 16bit map?
>
> Best,
> Junha Song.
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