<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear All-<div><br></div><div>Michael Held (ETH Zurich) wrote this comment about Python implementation of Bio-Formats. Any comments, feedback, or other similar experiences out there?</div><div><br></div><div>In general, our own preference would be to ensure there is a **single** resource for file format translation. Maintaining more than one just duplicates effort on something that is very difficult and tedious, even at the best of times. While I do agree that making a Python HCS-only reader is possible, and probably not terribly hard, it's the maintenance and updates of this resource that is really time consuming in the end. Until the various vendors coalesece around a single standard, that is just true. So, if possible, let's reuse as much as we have, and work together on a **single** resource, whatever it is.</div><div><br></div><div>Regarding the timings quoted, I'll let Curtis respond, but something sounds pretty wrong.</div><div><br></div><div>Comments??</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><div><br></div><div><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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; ">- The access to image formats via the Java-based bioformats has a big performance issue when accessing from C++/Python (or any non-Java system). People at Sybit/Switzerland tried there own Jace-based wrapper via BLITZ (libBlitzBioFormats), but had to improve Jace first, since the import of ONE! 512x512 image took ~60s. CellProfiler has its own way by launching a Java VM from Python.<span class="Apple-converted-space"> </span><br>The simple question behind this is: how to make the access to bioformats simpler and faster, which is an issue for the growing Python community.<br>I see two solutions for that.<br>1. Using the CellProfiler implementation as a standalone package. Performance is unknown to me. Short term issue.<br>2. I was wondering with Carolina Wählby from the Broad how much work it really is to collect the most needed formats for HC/HT screening and rewrite bioformats as a pure C++ library using the highly developed libtiff/libpng/libjpeg while providing a Python interface. For TIFF derivate formats (and there are many) this would be a simple job and there a C++ libs out there solving the problem already.<span class="Apple-converted-space"> </span><br>I guess CellProfiler has the same problem. Any opinions?<br></span></blockquote></div><br></div><br><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;"><span class="Apple-style-span" style="font-size: medium;"><br></span></span></font><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; "><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></body></html>