[SCIFIO] Bio-Formats Imaris writer

Wed Jul 16 15:32:20 CDT 2014

Hi Henry,

> 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.

Agreed, it should not be necessary to create Reader or Parser components.
However, writer-only components are still a little rough around the edges.
The relevant issue is:

https://github.com/scifio/scifio/issues/211

Feel free to comment on that so that GitHub sends you updates if you care
about progress on it.

But in the meantime, it should still be possible to create a writer-only
component. For an example, see the JavaFormat:

https://github.com/scifio/scifio/blob/scifio-0.15.4/scifio/src/main/java/io/scif/formats/JavaFormat.java

Regards,
Curtis

On Wed, Jun 25, 2014 at 1:21 PM, Henry Pinkard <henry.pinkard at gmail.com>
wrote:

> 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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