[SCIFIO] Bio-Formats Imaris writer

[Curtis Rueden]

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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