Question about Hamamatsu DCIMG format

[Adam Glaser]

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Hi everyone,

We use the Hamamatsu ORCA sCMOS cameras for our microscopy systems and stream the data to disk in the Hamamatsu DCIMG file format.  

In order to post-process and analyze our images, we have to first convert the DCIMG files to TIFFs.  We are currently using a MATLAB MEX file from Hamamatsu for the file conversion, but we are hoping to migrate everything to Python for increased speed, efficiency, and organization since our post-processing code is also in Python.  Unfortunately the MATLAB MEX file we have is a blackbox and of no use for re-writing in a different language.

I was wondering if anyone had or knew of any resources for DCIMG -> TIFF conversion in another language (Python, C++, Java, etc.)?

Thanks!

Adam

[Loralei Dewe-3]

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Hamamatsu will provide python drivers at no charge to their customers. In
addition, HC Image does let you save the files directly in tiff format if
you need to. Check the "help" function in HC Image.

Loralei

On Jun 9, 2017 2:41 PM, "Adam Glaser" <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi everyone,
>
> We use the Hamamatsu ORCA sCMOS cameras for our microscopy systems and
> stream the data to disk in the Hamamatsu DCIMG file format.
>
> In order to post-process and analyze our images, we have to first convert
> the DCIMG files to TIFFs.  We are currently using a MATLAB MEX file from
> Hamamatsu for the file conversion, but we are hoping to migrate everything
> to Python for increased speed, efficiency, and organization since our
> post-processing code is also in Python.  Unfortunately the MATLAB MEX file
> we have is a blackbox and of no use for re-writing in a different language.
>
> I was wondering if anyone had or knew of any resources for DCIMG -> TIFF
> conversion in another language (Python, C++, Java, etc.)?
>
> Thanks!
>
> Adam
>

[Adam Glaser]

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Thanks Loralei,

We are aware of the feature in HCImage but this is option is not conducive to automatic batch-processing of many DCIMG files for many datasets (as in our case).  I will contact Hamamatsu about the Python drivers - off hand do you know if these are simply to control the camera/data acquisition, or also to convert captured DCIMG files to more conventional image formats (such as TIFF).

Adam

[Loralei Dewe-3]

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I do not know the spwcifis.  Contact Hamamatsu technical support..

Loralei



On Jun 11, 2017 10:36 AM, "Adam Glaser" <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Thanks Loralei,
>
> We are aware of the feature in HCImage but this is option is not conducive
> to automatic batch-processing of many DCIMG files for many datasets (as in
> our case).  I will contact Hamamatsu about the Python drivers - off hand do
> you know if these are simply to control the camera/data acquisition, or
> also to convert captured DCIMG files to more conventional image formats
> (such as TIFF).
>
> Adam
>