This is a webpage used to present Image Analysis problems to the broader community. https://call4help.let-your-data-speak.com/ Thu, 09 Mar 2017 08:44:09 -0800 https://call4help.let-your-data-speak.com/blog/marta-alabrudzinska-karolinska-institutet https://call4help.let-your-data-speak.com/blog/marta-alabrudzinska-karolinska-institutet <a href=https://call4help.let-your-data-speak.com/blog/marta-alabrudzinska-karolinska-institutet>Read More</a> Thu, 09 Mar 2017 08:43:36 -0800 https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the-7a2f912a-e6b3-422e-bf39-e3fd42a04487 https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the-7a2f912a-e6b3-422e-bf39-e3fd42a04487 <p><strong>Marta Alabrudzinska (Karolinska Institutet)</strong></p><p><strong>Presentation:</strong></p><p><strong><a href="https://docs.google.com/presentation/d/15zaVPnIQk_MMS-Z5XBumaCjF3mG1LwXnZwERLEveEyk/edit?usp=sharing">https://docs.google.com/presentation/d/15zaVPnIQk_MMS-Z5XBumaCjF3mG1LwXnZwERLEveEyk/edit?usp=sharing</a></strong></p><p><strong>Presentation:</strong></p><p><strong><a href="https://docs.google.com/presentation/d/15zaVPnIQk_MMS-Z5XBumaCjF3mG1LwXnZwERLEveEyk/edit?usp=sharing">https://docs.google.com/presentation/d/15zaVPnIQk_MMS-Z5XBumaCjF3mG1LwXnZwERLEveEyk/edit?usp=sharing</a></strong></p><a href=https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the-7a2f912a-e6b3-422e-bf39-e3fd42a04487>Read More</a> Thu, 09 Mar 2017 05:00:13 -0800 https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the <h3><p>Q&A</p></h3><p><strong>What are the tools to segment network structures in *3D*?</strong></p><p>Try ImarisXT and MATLAB for filling segmented hollow vessels.</p><p>What is the desired level of automated analysis vs manual corrections?<br>What are the properties of 3D skeletons which seems to be relevant for biological problems?<br>What are the features which can be extracted from current tools?<br>What are tools which allow to control quality of segmentation?<br>What are the tools for batching 3D image processing / analysis?<br>Are there tools to segment 3D cylinders (semantic segmentation)?<br>What are techniques to segment hollow tubes? Of different diameter?</p><p>Ask Bitplane to implement solution<br>Look at intersection of surface normals (Tischi), defining middle of vessels<br>Use tools from Graph Theory to analyse extracted network --- e.g. MATLAB’s biograph function<br>Consider using machine learning (dictionary based) for segmentation (talk also to Daniel Sage)<br> </p><p> </p><a href=https://call4help.let-your-data-speak.com/blog/intravital-imaging-and-4d-quantification-of-tumor-growth-and-the>Read More</a> Thu, 09 Mar 2017 05:00:09 -0800 https://call4help.let-your-data-speak.com/blog/quantification-of-cardiac-micro-structures-on-intact-whole-heart https://call4help.let-your-data-speak.com/blog/quantification-of-cardiac-micro-structures-on-intact-whole-heart <h3><p>Q&A's</p></h3><p><strong>Is the data size the actual first bottleneck? What are good tools to process big EM data? Opensource?</strong></p><p>Consider using machine learning (dictionary based) for segmentation. (talk also to Daniel Sage). Talk also to Willy Kuo, PhD student of <a href="http://interfacegroup.ch/member/vartan-kurtcuoglu/">Vartan Kurtcuoglu</a> at Uni. Zurich</p><p><strong>Collagen network quantification: counting? Thickness? everything?</strong></p><p>Treat myofibrils (or their skeleton) as time-series to pull out summary statistics.<br> </p><a href=https://call4help.let-your-data-speak.com/blog/quantification-of-cardiac-micro-structures-on-intact-whole-heart>Read More</a>