From stephen.fyip1 at gmail.com Fri Aug 3 10:12:59 2018 From: stephen.fyip1 at gmail.com (Stephen Yip) Date: Fri, 3 Aug 2018 09:12:59 -0500 Subject: Openslide libtiff.h question Message-ID: Dear Community, I am playing around w/ the libtiff.h library to convert a tiff image into j2k format. I suspect that the errors (see below) are due to data loss in one of the pyramid layers. Since the data loss is typically insignificant, does anyone know how to by-pass the error? Or to replace the missing data w/ "0" or data acquired from a different layer? Thank you very much! Errors: TIFFReadRawTile: Read error at row 4294967295, col 4294967295; got 18446744073709551615 bytes, expected 0. E0718 16:20:29.440285 BagOfTasksProcessor.cpp:66] Exception while processing a bag of tasks: Corrupted file (e.g. inconsistent MD5 hash) TIFFReadRawTile: Read error at row 4294967295, col 4294967295; got 18446744073709551615 bytes, expected 0. E0718 16:20:29.442426 BagOfTasksProcessor.cpp:66] Exception while processing a bag of tasks: Corrupted file (e.g. inconsistent MD5 hash) TIFFReadRawTile: Read error at row 4294967295, col 4294967295; got 18446744073709551615 bytes, expected 0. E0718 16:20:29.444385 BagOfTasksProcessor.cpp:66] Exception while processing a bag of tasks: Corrupted file (e.g. inconsistent MD5 hash) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: data_loss.png Type: image/png Size: 646954 bytes Desc: not available URL: From yves.sucaet at usa.net Fri Aug 3 17:07:54 2018 From: yves.sucaet at usa.net (Yves Sucaet) Date: Fri, 03 Aug 2018 23:07:54 +0200 Subject: Come discuss computational pathology in Athens (CPW2018) In-Reply-To: References: Message-ID: <777wHcVg35344Set.1533330474@web07.cms.usa.net> Submission deadline for abstracts has been extended until August 15. When? Sunday, September 9, 2018. Where? Athens, Greece (during ECCB2018) Website? http://cpw2018.org Digital and computational pathology are increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities. This second edition is organized as a full-day workshop during ECCB 2018 (http://www.eccb18.org). KEYNOTE SPEAKERS: The following keynote speakers are confirmed to speak at the conference: Thomas Fuchs, Memorial Sloan Kettering Cancer Center Chakra Chennubhotla, University of Pittsburgh Derek Magee, University of Leeds SUBMISSIONS: The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. Conference proceedings will be published by the Journal of Pathology Informatics. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to https://www.fourwav.es/cpw2018 SCOPE: Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list): Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman,...)... Research applications on non-human model organisms KEY DATES: Submission deadline: August 15, 2018. Conference: Sunday September 9, 2018. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Memorial Sloan Kettering Cancer Center, USA Rapha?l Mar?e, Universit? de Li?ge, Belgium David Ameisen, IRIF, CNRS and Universit? Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands Jeffrey Fine, Magee-Womens Hospital of UPMC