<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear All-<div><br></div><div>Another comment forwarded from Michael held (ETH Zurich):</div><div><br></div><div>"Despite the use of the OMERO database the points of storing data in a more convenient/performant/flexible HDF5/netCDF4 format is very pressing. This could also include the raw image data, since storage of millions single TIFF is problematic in many ways. Josh mentioned something like a OME-HDF4/netCDF4 format. At least for the raw data we should make sure that tools like ImageJ will support this format. "</div><div><br></div><div>We've discussed using HDF as an image file format for some time. We already use HDF5 for storing tabular data in OMERO (<a href="http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTables">http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTables</a>). There are many obvious advantages to using an HDF5 data store, namely flexible in data structures that can be stored. These have been summarised recently (<a href="http://queue.acm.org/detail.cfm?id=1628215">http://queue.acm.org/detail.cfm?id=1628215</a>).</div><div><br></div><div>However, the limited case mentioned above-- too many single TIFFs- doesn't seem to be a good argument for creating yet another image file format. There are many ways to alleviate the problem of millions of TIFFs. the easiest one is to use multi-page TIFFs (as in, for example, OME-TIFF). The optimization and stability of TIFF readers shouldn't be forgotten. Obviously, other data types, especially analysis data etc. won't fit into this data format, at least not easily. Are they strong arguments for choosing HDF etc. purely as a multi-plane store over TIFF-based formats?</div><div><br></div><div>As is hinted above, putting other data types into image files will require adaptation of the various applications to actually use this data. Again, not a small effort.</div><div><br></div><div>My two cents-- any other thoughts? We would love to hear strong arguments to invest in and HDF-based image file format. </div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: <a href="http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html">http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span> </div><br></div></body></html>