[SCIFIO] Bio-Formats Imaris writer

[Henry Pinkard]

Hi Curtis,

This all sounds great. I've cloned the SCIFIO core as well as the
tutorials, which have been quite helpful in getting things set up.

I've created a class in the io.scif.formats package for my writer. Since I
only have the writer components, but not the reader, how should I go about
implementing all of the component classes of Format (Metadata, Parser,
Checker, Reader, Writer, Translator). The first 4 are listed as mandatory
in the tutorial, but it seems like I shouldn't need all of them for writing
functionality alone.

Best,
Henry


On Sun, Jun 1, 2014 at 7:27 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Henry,
>
> > Over the past couple years, I've been developing and testing a java
> > library that is capable of writing Imaris .ims files. This library has
> > allowed me to build an ImageJ plugin that automatically stitches,
> > processes, and converts OME-TIFFs from Micro-Manager into Imaris
> > files, which in turn allows a significantly greater throughput of
> > imaging data with much less effort from users.
>
> Sounds great!
>
> > This library has been instrumental to the workflow of users in the
> > imaging center in which I work, and I want to find a way to share its
> > utility with researchers everywhere. Incorporating it into the
> > Bio-Formats exporter would both increase its visibility and leverage
> > the multitude of formats on Bio-Formats' front end to make it usable
> > with all types of microscopy data.
>
> Rather than implementing a Bio-Formats writer, I encourage you to check
> out SCIFIO [1, 2, 3]. Though still in beta, SCIFIO is the core I/O
> mechanism of ImageJ2, which is finally due for release later this week.
> SCIFIO uses the SciJava plugin framework, meaning your writer would be
> automatically discovered and used as appropriate with no additional work
> from you. And we have recently integrated SCIFIO directly into ImageJ at
> the core level, so things like File > Open now use it, including whatever
> format plugins are available. (SCIFIO also has a Bio-Formats format plugin,
> so that all of the BF formats work in ImageJ that way, too!)
>
> You could then serve your Imaris writer from its own ImageJ update site
> [4, 5], to make it available to all ImageJ users.
>
> > In addition, I've convinced Bitplane to make their format open source,
> > and I believe this may allow .ims files to grow beyond a proprietary
> > file format into a generalized multi-resolution format useful for a
> > variety of applications that deal with the visualization of extremely
> > large stitched images.
>
> Glad to hear that Bitplane is willing to do this. In that case, if you do
> complete a SCIFIO Imaris writer and want to donate the code upstream, you
> could file a pull request against the SCIFIO LifeSci project [6] to
> contribute it there, since that project houses readers & writers for _open_
> life sciences formats. So if Bitplane publishes an open specification, we
> would be willing to add it to the project.
>
> If you have any questions about SCIFIO, please feel free to use the SCIFIO
> mailing list [7]. Or if you go the Bio-Formats route, you can use ome-devel
> [8].
>
> Regards,
> Curtis
>
> [1] http://loci.wisc.edu/software/scifio
> [2] https://github.com/scifio/scifio
> [3] https://github.com/scifio/scifio-tutorials
> [4] http://wiki.imagej.net/Update_Sites
> [5] http://wiki.imagej.net/List_of_update_sites
>  [6] https://github.com/scifio/scifio-lifesci
> [7] http://scif.io/mailman/listinfo/scifio
> [8] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel/
>
>
> On Thu, May 29, 2014 at 6:55 PM, Henry Pinkard <henry.pinkard at gmail.com>
> wrote:
>
>> Hi Melissa and Curtis,
>>
>> Over the past couple years, I've been developing and testing a java
>> library that is capable of writing Imaris .ims files. This library has
>> allowed me to build an ImageJ plugin that automatically stitches,
>> processes, and converts OME-TIFFs from Micro-Manager into Imaris files,
>> which in turn allows a significantly greater throughput of imaging data
>> with much less effort from users.
>>
>> This library has been instrumental to the workflow of users in the
>> imaging center in which I work, and I want to find a way to share its
>> utility with researchers everywhere. Incorporating it into the Bio-Formats
>> exporter would both increase its visibility and leverage the multitude of
>> formats on Bio-Formats' front end to make it usable with all types of
>> microscopy data. In addition, I've convinced Bitplane to make their format
>> open source, and I believe this may allow .ims files to grow beyond a
>> proprietary file format into a generalized multi-resolution format useful
>> for a variety of applications that deal with the visualization of extremely
>> large stitched images. I'm happy to rework the library in whatever ways
>> make it easiest to incorporate on your end. Let me know your thoughts on
>> how to best proceed.
>>
>> Best,
>> Henry
>>
>
>
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