<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi All,</div><div class=""><br class=""></div><div class="">I have 2 problems you all hopefully have suggestions for... (thanks in advance)</div><div class=""><br class=""></div><div class=""><b class="">Problem 1:</b></div><div class=""><br class=""></div>I'm interested in opening ND2 file format programmatically in Java via a SCIFIO object used with an ImageJ context but can't seem to get it to work. (see listing A) Error message indicates format not found.<div class=""><div class=""><br class=""></div><div class="">Hopefully relevant details of what I am currently doing with maven imports are below. (see listing B)</div><div class=""><br class=""></div><div class="">Suggestions? Is there a BioFormats dependency I am not bringing in that is necessary to expose/discover all the additional proprietary formats or do I have to add the proprietary formats myself using a combination of a bioformats artifact I'm not aware of and adding each format using the mechanism provided by scifio-bf-compat? I thought it used to be automatic upon adding the scifio and scifio-bf-compat dependencies. Any help is appreciated. I looked in scifio tutorials but couldn't figure it out. Sorry.</div><div class=""><br class=""></div><div class=""><b class="">Problem 2:</b></div><div class=""><br class=""></div><div class="">After resolution of problem 1, I'd like to leverage recent changes to the bioformats package that addresses a bug in ND2 metadata handling that was affecting me (<a href="https://trac.openmicroscopy.org.uk/ome/ticket/12548" class="">https://trac.openmicroscopy.org.uk/ome/ticket/12548</a>). The link suggests using bioformats 5.1.x vs 5.0.x which also requires use a few other updated jars (as noted near end of ticket). Suggestions on the best way to do this given my use case? It looks like the parent pom of scifio-bf-compat (pom-scijava) specifies <bio-formats.version>5.0.7</bio-formats.version>. Is it likely to be "risky" to leverage the most recent changes for ND2 compatibility?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">Jay</div><div class=""><br class=""></div><div class="">%%%%%%%%%%%%%</div><div class="">Listing A</div><div class="">%%%%%%%%%%%%%</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""><span style="color: rgb(147, 26, 104);" class="">final</span> SCIFIO scifio = <span style="color: rgb(147, 26, 104);" class="">new</span> SCIFIO(<span style="color: rgb(3, 38, 204);" class="">ij</span>.getContext());</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">Reader reader;</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(147, 26, 104);" class="">try</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">{</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>reader = scifio.initializer().initializeReader(nd2File, <span style="color: rgb(147, 26, 104);" class="">new</span> SCIFIOConfig().checkerSetOpen(<span style="color: rgb(147, 26, 104);" class="">true</span>));</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">}</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""><span style="color: rgb(147, 26, 104);" class="">catch</span> (Exception e)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">{</div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>e.printStackTrace();</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(147, 26, 104);" class=""><span style="color: rgb(0, 0, 0);" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span></span>return<span style="color: rgb(0, 0, 0);" class=""> </span>false<span style="color: rgb(0, 0, 0);" class="">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class="">}</div></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><div class="">%%%%%%%%%%%%%</div><div class="">Listing B</div><div class="">%%%%%%%%%%%%%</div></div><div class=""><br class=""></div><div class="">My project parent pom is </div><div class=""><br class=""></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #009193" class=""><span class="Apple-tab-span" style="white-space:pre"> </span><</span>parent<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>groupId<span style="color: #009193" class="">></span><span style="color: #000000" class="">net.imagej</span><span style="color: #009193" class=""></</span>groupId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>artifactId<span style="color: #009193" class="">></span><span style="color: #000000" class="">pom-imagej</span><span style="color: #009193" class=""></</span>artifactId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>version<span style="color: #009193" class="">></span><span style="color: #000000" class="">5.12.0</span><span style="color: #009193" class=""></</span>version<span style="color: #009193" class="">></span></div><div class=""><span style="font-family: Monaco; font-size: 11px;" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="font-family: Monaco; font-size: 11px; color: rgb(0, 145, 147);" class=""></</span><span style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px;" class="">parent</span><span style="font-family: Monaco; font-size: 11px; color: rgb(0, 145, 147);" class="">></span></div><div class=""><br class=""></div><div class=""> I have the following maven dependencies</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #009193" class=""><span class="Apple-tab-span" style="white-space:pre"> </span><</span>dependency<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>groupId<span style="color: #009193" class="">></span><span style="color: #000000" class="">io.scif</span><span style="color: #009193" class=""></</span>groupId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>artifactId<span style="color: #009193" class="">></span><span style="color: #000000" class="">scifio</span><span style="color: #009193" class=""></</span>artifactId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""></</span>dependency<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>dependency<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>groupId<span style="color: #009193" class="">></span><span style="color: #000000" class="">io.scif</span><span style="color: #009193" class=""></</span>groupId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""><</span>artifactId<span style="color: #009193" class="">></span><span style="color: #000000" class="">scifio-bf-compat</span><span style="color: #009193" class=""></</span>artifactId<span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco;" class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #009193" class=""><</span><span style="color: #4e9192" class="">scope</span><span style="color: #009193" class="">></span>runtime<span style="color: #009193" class=""></</span><span style="color: #4e9192" class="">scope</span><span style="color: #009193" class="">></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: #000000" class=""><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #009193" class=""></</span>dependency<span style="color: #009193" class="">></span></div></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">A "limited" list of 30 formats show up in the DefaultFormatService currently and don't include ND2. (see Listing C)</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">%%%%%%%%%%%%%</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">Listing C</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">%%%%%%%%%%%%%</div></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">(*) Formats in DefaultFormatService</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 145, 146);" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px;" class=""><div style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px; margin: 0px;" class="">ImageJ ij = <span style="color: #931a68" class="">new</span> ImageJ();</div><div style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px; margin: 0px;" class="">Set<Format> <span style="text-decoration: underline" class="">formats</span> = ij.scifio().format().getAllFormats();</div><div style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px; margin: 0px;" class=""><br class=""></div><div style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px; margin: 0px;" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class="">returns</span></div><div style="color: rgb(78, 145, 146); font-family: Monaco; font-size: 11px; margin: 0px;" class=""><span style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;" class=""><br class=""></span></div><div style="margin: 0px;" class="">[Bio-Formats Compatibility Format, Animated PNG, Audio Video Interleave, Windows Bitmap, DICOM, Encapsulated PostScript, Flexible Image Transport System, Simulated data, Graphics Interchange Format, Image Cytometry Standard, JPEG-2000, JPEG, Java source code, Multiple Network Graphics, Micro-Manager, NRRD, OBF, PCX, Portable Gray Map, Text, Zip, QuickTime, PICT, plugin:class io.scif.ome.formats.OMEXMLFormat, Tile JPEG, QuickTime, plugin:class io.scif.ome.formats.OMETIFFFormat, Tagged Image File Format, Minimal TIFF, Tagged Image File Format]</div><div style="margin: 0px;" class=""><br class=""></div><div style="margin: 0px;" class=""><br class=""></div></div></div></div></body></html>