[SCIFIO] New file format for SCIFIO

[Mark Hiner]

Hi Jerome,

 It's great to hear your interest in integrating your format with SCIFIO
and ImageJ2. I'm copying this mail to the SCIFIO mailing list, as this
would be of interest and benefit to the community.

>I hope you could add this the the SCIFIO or explain me where to integrate
this modification.

 There is a SCIFIO component, SCIFIO-tutorials
<https://github.com/scifio/scifio-tutorials>, which was designed to
introduce the API to developers. In particular, the Custom Format
<https://github.com/scifio/scifio-tutorials/blob/master/core/src/main/java/io/scif/tutorials/core/T3aCustomFormats.java>
tutorial and studying a simple existing format
<https://github.com/scifio/scifio/blob/master/src/main/java/io/scif/formats/PCXFormat.java>
would be the recommended starting point. If anything is unclear in these
tutorials or if you have further questions about how the SCIFIO format
should be structured, please feel welcome to ask questions on this list,
and to report issues on GitHub.

 Once you have a SCIFIO reader for your format, you can distribute it to
users via an update site
<http://imagej.net/How_to_set_up_and_populate_an_update_site>.

 With a little work <https://github.com/scifio/scifio-bf-compat/issues/4>
on my part, your new SCIFIO reader will get picked up by Bio-Formats, which
will then allow it to work in Stitching.

 We're happy to provide any guidance we can - looking forward to your
contributions and feedback!

Regards,
Mark

On Fri, Sep 12, 2014 at 7:01 AM, Jérôme Parent <jerome.parent at lynceetec.com>
wrote:
>
> Hello,
> I am working for Lynceetec a Swiss company that develop and manufacture
> Digital Holographic Microscope (DHM). This microscope are used in Life and
> Material Science.
> In the past I have written a plugin for ImageJ 1 to read our file format
> .bin file (attached to this email).
> There is a new class Koala_Bin_Reader and the file
> HandleExtraFileTypes.java is updated. This plugin works fine in ImageJ 1
>
> Now I wonder if we can integrate this reader to SCIFIO and ImageJ2 to
> improve our user experience.
>
> The Stitching of Fijii is powerfull but the stitching module cannot load
> our binary format because is not currently supported in Fijii.
>
> I hope you could add this the the SCIFIO or explain me where to integrate
> this modification.
>
> Congratulations for the great job and contribution to ImageJ project, I
> use it for a long time and love it.
>
> Best Regards,
> Jerome
>
> *Jérôme Parent*
> Area Sales Manager
> Office : 0041 21 693 02 27
> Mobile : 0041 79 193 91 69
> www.lynceetec.com
>
> *Lyncée Tec SA*
> PSE-A
> CH-1015 Lausanne
> Switzerland
>
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