<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Thanks for your reply.<div class=""><br class=""></div><div class="">I was able to print out the actual error:</div><div class=""><br class=""></div><div class=""><div class="">Cannot read this file because your OS vendor ships a modified version of OpenJPEG with broken support for chroma-subsampled images. OpenJPEG error: Error decoding tile. Component 1 contains only 32768 blocks while component 0 has 65536 blocks</div></div><div class=""><br class=""></div><div class="">Then I searched for this error and found out it is due to OpenJPEG patch.</div><div class=""><br class=""></div><div class="">I have OpenJPEG 1.5.1-10.el7, OpenSlide 3.4.1-.el7 installed on my RedHat server.</div><div class=""><br class=""></div><div class="">Should I <b class="">downgrade</b> OpenJPEG to a version lower than 1.3.1 as suggested in the bug post: </div><div class=""><br class=""></div><div class=""><a href="https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-March/000751.html" class="">https://lists.andrew.cmu.edu/pipermail/openslide-users/2014-March/000751.html</a></div><div class=""><br class=""></div><div class="">OR…. should I upgrade OpenJPEG to 2.1.0????</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 22, 2016, at 3:34 PM, Rogers, David W <<a href="mailto:drogers@fredhutch.org" class="">drogers@fredhutch.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Openslide documentation indicates that all levels other than level 0 are ignored for some formats, e.g., Hamamatsu. Perhaps it is the same for Aperio?<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">--<br class="">David W. Rogers<span class="Apple-converted-space"> </span><br class="">Software Developer / Collaborative Data Services / 206.667.7089 / drogers</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">@</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://fredhutch.org/" style="color: purple; text-decoration: underline;" class="">fredhutch.org</a><span class="Apple-converted-space"> </span>/ Fred Hutch / Cures Start Here</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div class=""><div style="border-style: solid none none; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>openslide-users [<a href="mailto:openslide-users-bounces+drogers=fredhutch.org@lists.andrew.cmu.edu" class="">mailto:openslide-users-bounces+drogers=fredhutch.org@lists.andrew.cmu.edu</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Ginger Han via openslide-users<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, March 22, 2016 11:54 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:openslide-users@lists.andrew.cmu.edu" class="">openslide-users@lists.andrew.cmu.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Failed to get correct layer count for Aperio images<o:p class=""></o:p></span></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Hello,<o:p class=""></o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">I have a collection of Aperio whole slide images of digital pathology. None of them was successfully read using OpenSlide C API functions. <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">For example, with <span style="font-size: 8.5pt; font-family: Menlo, serif; color: rgb(88, 126, 168);" class="">openslide_get_level_count()</span> I only get -1 for layer count indicating that the reading was not right.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">However, ALL of them can be opened using Aperio ImageScope without any problem.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Please help!!!!</div></div></div></div></blockquote></div><br class=""></div></body></html>