[SCIFIO] Bio-Formats Imaris writer

[Henry Pinkard]

Hi Curtis and Mark,

Finally back to work on this project. I've created an ImarisFormat class in
my local copy of SCIFIO and have gotten a basic version of
ImarisFormat.Writer working. Several questions regarding this:

1) Since .ims files are a specific type of HDF5 file, I'm utilizing the HDF
Java library to do the writing. Maven is able to record a dependency for
the .jar file needed by this library, but I'm not sure how to indicate a
dependency on the the native files that the library uses through the JNI.
For testing purposes I just copied these libraries into the SCIFIO root
directory, but this is obviously not a solution. I assume that there is an
elegant way of doing this, since the BioFormats Imaris reader is able to
read these files. Any thoughts?

2) I'm unsure whether to have the writer extend AbstractWriter or simply
implement TypedWrtier. I would think that AbstractWriter is provided as a
stub to easily extend when making writer classes, but the private access to
all of this classes field's (metadata, initialized, etc.) mean that I have
to extend many more methods than I would like. Could these fields be made
protected, or should I switch to TypedWriter and have a lot of empty,
irrelevant methods?

3) I'm able to pull all the metadata required for writing these files from
DefaultMetadata and DefaultImageMetadata, with the exception of two things.
First, is there a way to get the acquisition date and timestamps form
individual planes? Second, the config.writerGetColorModel() call that I
copied from AbstractWriter returns null, as does plane.getColorTable(). Is
there some other way to get image lookup tables? My test code opens a Tiff
stack saved by FIJI that has LUTs applied, so I would think they would be
there. Is there another mechanism for getting image LUTs?

Excited to see this writer become part of SCIFIO in the near future.

Best,
Henry

On Wed, Jul 16, 2014 at 4:32 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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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