tag:blogger.com,1999:blog-15942814887260501502024-02-22T21:31:58.716+10:00TissueStack is awesomeUnknownnoreply@blogger.comBlogger32125tag:blogger.com,1999:blog-1594281488726050150.post-70186110576627405072015-06-23T13:59:00.006+10:002015-06-23T14:00:48.619+10:00Version 2.1Binaries can be downloaded from here:<br />
<br />
<a href="http://tissuestack.org/downloads/" target="_blank">http://tissuestack.org/downloads/</a><br />
<a href="http://tissuestack.com/downloads/" target="_blank">http://tissuestack.com/downloads/</a>haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-33184607217105719262015-05-08T10:26:00.002+10:002015-05-08T10:26:25.001+10:00Version 2.0<u><b>Version 2.0 implements support for dicom format</b></u><br />
<br />
<br />
Both, the offline as well as the online converter tool can now convert dicom files to Tissue Stack's internal raw format via dcmtk (<a href="http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Overview" target="_blank">http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Overview</a>)<br />
<br />
<br />
Supported are:<br />
<br />
<ul>
<li>gray-scale data of various bit depth</li>
<li>color data</li>
</ul>
<div>
<br /></div>
<div>
"Partially" supported are:</div>
<ul>
<li>Siemens mosaic files which will be (for now at least) displayed in the same way a time series would</li>
<li>In Multi-Frame only the first frame will be considered.</li>
</ul>
<div>
Both of the limitations above are, in part, due to the display modalities of Tissue Stack which is inherently 3D.</div>
<br />
<br />
<br />
NOTE: jpeg 2000 compression is not supported<br />
<br />
<br />
<u><i>How to prepare dicom data for Tissue Stack conversion?</i></u><br />
<br />
Single images can just be used/uploaded as are.<br />
<br />
Series have to be zipped with the requirement that there only be one per zip and no sub-directories be used within the zip!<br />
<br />
<br />
<br />
<u>FURTHER NOTES:</u><br />
<u><br /></u>
Both, the offline and online converter will unzip the contents of the zip into the /tmp directory using the zip name as a subdirectory.<br />
<br />
Conversion may take a while depending on factors such as size of zip, use of compression, and type of data. In general, single images (obviously) and data interpreted as time series (incl. Siemens mosaic) will be much quicker than anything else which will be reconstructed into a 3D volume.<br />
<br />
<br />
<u>BINARY PACKAGES:</u><br />
<br />
<a href="http://tissuestack.org/downloads/" target="_blank">http://tissuestack.org/downloads/</a><br />
<a href="http://tissuestack.com/downloads/" target="_blank">http://tissuestack.com/downloads/</a>haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-56739437777491283532015-03-06T09:20:00.004+10:002015-03-06T09:20:51.960+10:00Version 1.9<br />
<u><b><br /></b></u>
<div style="text-align: center;">
<u><b>Version 1.9</b></u> contains bug-fixes for the previous version and is highly recommended.</div>
<br />
<br />
<br />
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
or:</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a></div>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-16931226583237235352015-02-19T10:36:00.000+10:002015-02-19T10:36:04.149+10:00Version 1.8<br />
This version includes support for displaying anisotropic data sets.<br />
<br />
This feature has to still be considered somewhat beta since it has not yet been tested extensively, particularly the case where all three dimensions are not isotropic respectively.<br />
<br />
Binary packages can be downloaded here:<br />
<br />
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a><br />
<br />
or<br />
<br />
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a>haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-73055966300245459852015-01-28T16:36:00.002+10:002015-01-28T16:37:15.685+10:00Version 1.7Version 1.7 includes bug-fixes and an upgrade of jquery and jquery mobile.<br />
<br />
Binary Packages can be downloaded here: <a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a>haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-48367955771561209532014-10-02T18:53:00.004+10:002014-10-03T18:11:34.432+10:00Version 1.5<b><u><br /></u></b>
<b><u><br /></u></b>
<b><u>Version 1.5</u></b> is the result of a major re-factoring effort.<br />
<div>
<br /></div>
<div>
<br />
The former C ImageServer component has been rewritten entirely in C++ and also replaced functionality that was java code.</div>
<div>
<br /></div>
<div>
<br />
It is now also responsible for the configuration database and database communication as well as the http based application requests, in summation everything but the front-end bits of TissueStack.</div>
<div>
<br />
<br /></div>
<div>
Along the way a good deal of optimization measures were implemented and more are to come such as the memory-caching of image tiles to speed up on-the-fly tiling.</div>
<div>
<br />
<br /></div>
<div>
TissueStack binary packages have become much smaller since no java run-time is used any more, nor any application server is needed. JNI and inter-component communication through unix sockets is history as well.</div>
<div>
<div>
<br />
<br /></div>
</div>
<div>
<u>Also:</u> The offline pre-tiler and conversion tools got renamed. They need to be called like this:<br />
<br />
<blockquote class="tr_bq">
<i>TissueStackConverter -i IN_FILE (*.mnc,*.nii,*.nii.gz) -o OUT_FILE</i></blockquote>
<blockquote class="tr_bq">
<i>TissueStackPreTiler -d DIMENSION_NAMES -l LEVELS [-c COLORMAP] -p PATH -f FILE </i></blockquote>
The conversion is done in parallel by three processes (1 per dimension) if the platform has 3 cores or more. The pre-tiling is fine-grained enough (see command-line parameters) such that it can be started in parallel easily.<br />
<br />
<div style="text-align: center;">
***</div>
<br />
<br /></div>
<div>
The new binaries can be found at:</div>
<div>
<br /></div>
<div>
http://tissuestack.com/downloads </div>
<div>
<br /></div>
<div>
or:</div>
<div>
<br /></div>
<div>
http://tissuestack.org/downloads</div>
<div>
<br /></div>
<div>
<u><b><br /></b></u></div>
<div>
<u><b><br /></b></u></div>
<div>
<u><b><br /></b></u></div>
<div>
<u><b>Installation Notes:</b></u></div>
<div>
<br /></div>
<div>
The <u>debian package</u> has been built/tested on Ubuntu 14.04. It is very likely that it is not compatible with the latest Debian versions for differences in library versions that TissueStack depends on and/or apache/postgres configuration differences. On the plus side all dependencies can be gotten through the Ubuntu 14.04 repositories which is not the case for the redhat based distros (see below).</div>
<div>
<br /></div>
<div>
The install procedure is slightly tedious and involves the following steps:</div>
<div>
sudo apt-get install apache2 postgresql [to get dependencies that need to be configured beforehand]</div>
<div>
sudo dpkg -i tissuestack_1.5_amd64.deb [which will fail, so don't be surprised!]</div>
<div>
sudo apt-get install -f [which will deal with the causes of failure in the step above]</div>
<div>
<br /></div>
<div>
<br /></div>
<div>
<br /></div>
<div>
There is now an <u>el6 version</u> which was built and tested on CentOS 6.5.</div>
<div>
It requires you to also download and install the builds of nifticlib (2.0.0) and minc (2.1.0) which can be found in the same location as the tissuestack rpm.</div>
<div>
<br /></div>
<div>
The <u>Fedora 19 package</u> only needs the minc (2.1.0) rpm to be installed which again can be found in the same location.<br />
<br />
**** UPDATE *****<br />
<br />
There is now also a Debian 7 and an OpenSUSE 13.1 package in the respective directories.</div>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-49664656229725143952014-04-15T15:26:00.000+10:002014-04-15T15:36:18.850+10:00new Version 1.4 available<b><u><br /></u></b>
<b><u>Latest Changes:</u></b><br />
<br />
The internal .raw format used by Tissue Stack will store data as 8bit RGB triples while before it was limited to 8 bit grayscale.<br />
<br />
<br />
<i><u>This immediately leads to the following advantages:</u></i><br />
<br />
<ul>
<li>Usage of RGB minc and NIFTI formats as input data is now possible.</li>
<li>On-the-fly image generation for a data set that frequently uses a color map may be replaced by a color data set instead.</li>
<li>Label Lookups can make use of the much larger space of lookup values (over 16 million), for instance volumes pointing to structure information encoded via RGB triples are not limited to represent 256 structures only.</li>
</ul>
<div>
<br /></div>
<i><u>Notes:</u></i><br />
<div>
<ul>
<li>Data Sets already converted and in use by Tissue Stack instances will still be compatible.</li>
<li>If you use RGB MINC files as input, the expected order is: spatial dimensions first, RGB channels are represented by the 4th dimension (length: 3).</li>
<li>If you use color NIFTI files, the required dimension layout is as follows: There are 3 spatial dimensions followed by a time dimension which will have length 1 in the simplest case with the RGB channels contained in the next dimension (length: 3)</li>
</ul>
<div>
<br /></div>
</div>
<div>
<i><u>Binary Installs (only 64bit):</u></i></div>
<div>
<i><u><br /></u></i></div>
<div>
Debian packages (compiled and tested on Ubuntu 12.10), Fedora rpms (compiled and tested on Fedora 19) and epel rpms (compiled and tested on CentOS 6.4) can be downloaded from either one of the following locations:</div>
<div>
<br /></div>
<div>
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a></div>
<div>
<br /></div>
<div>
or</div>
<div>
<br /></div>
<div>
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a></div>
<div>
<br /></div>
<div>
For the fedora packages you will need to download and install the minc library as well (same locations provided above).</div>
<div>
The epel rpms require you to add the following repository to /etc/yum.repos.d in order to be able to satisfy the dependencies needed: <a href="http://cvlrepo.massive.org.au/repo/cvl.repo">http://cvlrepo.massive.org.au/repo/cvl.repo</a></div>
<div>
<br /></div>
<div>
<br /></div>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-85180362408647909132013-10-24T12:47:00.000+10:002013-11-01T12:39:53.957+10:00Version 1.3 is outThis version includes the following:<br />
<br />
<ol>
<li>bug-fixes regarding contrast and color map behavior</li>
<li>label lookup files can be used for a discrete colormap as well</li>
<li>user interface changes in regards to data set information</li>
</ol>
<div>
<b><u><br /></u></b></div>
<div>
<b><u>2. label lookup files can be used for a discrete color map:</u></b></div>
<div>
<b><u><br /></u></b></div>
<div>
So far a text file of the following layout could be used to associate lookup information with pixel values:</div>
<div>
<br /></div>
<br />
<blockquote class="tr_bq">
0 0 0 0 Black (Background)<br />
1 106 114 188 A24a<br />
2 106 114 158 A24a'<br />
3 116 107 219 A24b</blockquote>
<div>
<br /></div>
<div>
The first column will be the gray scale value for the lookup, then come the 3 RGB columns and last is the text associated with the previous 4.</div>
<div>
<br /></div>
<div>
<br /></div>
<div>
The crucial steps to using the above lookup table are:</div>
<div>
<ol>
<li>Make sure the colums are separated by tabs !!</li>
<li>Place the file into the lookup folder of the data directory, i.e. <i>/opt/tissuestack/lookup</i></li>
<li>Restart the service, e.g. /etc/init.d/tissuestack restart (as super user)</li>
</ol>
<div>
Once this has been done, the drop down menu for the color map will include the lookup files color mapping. It will display as its file's name.</div>
</div>
<div>
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4ISb52tCTuWzg_i8lMvnt218yS1YIbS4yrb3uofOryRr3u1ThSTPpIcvQS6KlrrfvtcHaB01Q-vQr5OBT3k_Wu364Ve04c-eCsTcVOam0bLPwle6lywEb27mKPTMnqueEY8Ami-rdkwpI/s1600/labels.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="96" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4ISb52tCTuWzg_i8lMvnt218yS1YIbS4yrb3uofOryRr3u1ThSTPpIcvQS6KlrrfvtcHaB01Q-vQr5OBT3k_Wu364Ve04c-eCsTcVOam0bLPwle6lywEb27mKPTMnqueEY8Ami-rdkwpI/s400/labels.png" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div>
<br /></div>
<div>
<u>Side Note:</u> While the color map from the lookup file is available, one more step is required for the label/text to be shown as in the screenshot above.</div>
<div>
<br /></div>
<div>
The table <i>dataset_values_lookup </i>in the tissuestack database will have the contents of the lookup file information which might look like this:</div>
<div>
<br /></div>
<div>
</div>
<div>
<br /></div>
<div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtdBbGyRP9KlimV-V1KciMT7ERvZpU8fkxJIlNaZMETGKp9jfapF_KnJray8L8Ufwq6IxrrLwVgadPwHj8c5u-kYKPUxORVU1mejJbX3nnUOJwYGcXJtYL7JtcRP16XF1_GTHtRgyj7R2e/s1600/lookup.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="110" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtdBbGyRP9KlimV-V1KciMT7ERvZpU8fkxJIlNaZMETGKp9jfapF_KnJray8L8Ufwq6IxrrLwVgadPwHj8c5u-kYKPUxORVU1mejJbX3nnUOJwYGcXJtYL7JtcRP16XF1_GTHtRgyj7R2e/s400/lookup.png" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
Use the id to link it with the corresponding dataset in the table <i>dataset </i>by means of a simple sql update as such:</div>
<blockquote class="tr_bq">
UPDATE dataset SET lookup_id=? WHERE id=?</blockquote>
The question marks will have to be replaced by the desired ids.<br />
<br />
The result will be viewable after a reload/refresh of the web site.<br />
<br />
<br />
<b><u>3. user interface changes in regards to data set information map:</u></b><br />
<b><u><br /></u></b>
The navigation tree will use the description provided when add the data set will be added which makes for a nicer appearance than the previously used data set id and server location. This change also applies to the mobile interfaces of the tablet and the phone version. The desktop ought to look something like this:<br />
<b><u><br /></u></b>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGHeULlNNkyATDSdBt7KiIDpqzcaS56AW6ES4g5IEh82bkzRpB3wNQ_9fE4FETDRSTyF3R8lG4cL0XLfezDigW5YP8JJeJzVg2JviNzqYwpEB8P8qdx40p3cMk6QfSczmpRAFN8KLTGtcK/s1600/navigation.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGHeULlNNkyATDSdBt7KiIDpqzcaS56AW6ES4g5IEh82bkzRpB3wNQ_9fE4FETDRSTyF3R8lG4cL0XLfezDigW5YP8JJeJzVg2JviNzqYwpEB8P8qdx40p3cMk6QfSczmpRAFN8KLTGtcK/s320/navigation.png" width="141" /></a></div>
<b><u><br /></u></b>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZzqnU0-FvkiXdLvwfVfQg9-POWa5xVfr_s5Qv7oLc-LF-jSnUKDdzWtxJJGnQlWNyPFLP0l3fCXmQllb_5-SklMHahTcgD1p7yv9FfRU6iqbJDnl2mdhDWpHn4GKnSeG_GcRS0O424pBV/s1600/config.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="88" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZzqnU0-FvkiXdLvwfVfQg9-POWa5xVfr_s5Qv7oLc-LF-jSnUKDdzWtxJJGnQlWNyPFLP0l3fCXmQllb_5-SklMHahTcgD1p7yv9FfRU6iqbJDnl2mdhDWpHn4GKnSeG_GcRS0O424pBV/s320/config.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<u>Side Note:</u> Should there be a desire to edit the contents of the description field, this can be achieved by updating it in the database, in specific in the table dataset (which was mentioned above already):<br />
<br />
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
<u>A word of caution:</u> The filename column should not be updated/changed unless the source file did really get moved/renamed, otherwise the on-the-fly Image Server will be unable to locate it. Likewise the id of the dataset is used in the location determination of the tiling directory such that if it were updated the tiling directory associated with the data set would have to be renamed too.</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
***</div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
<i>Last but not least, the binary packages can be downloaded from:</i></div>
<div class="separator" style="clear: both; text-align: left;">
<i><br /></i></div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a></div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
<i>or </i></div>
<div class="separator" style="clear: both; text-align: left;">
<i><br /></i></div>
<div class="separator" style="clear: both; text-align: left;">
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a></div>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-78651163248670813522013-08-28T11:42:00.000+10:002013-11-01T12:41:00.849+10:00Version 1.2 availableThis version includes bug-fixes as well as the following 2 features:<br />
<br />
<blockquote class="tr_bq">
<ul>
<li>There is now an easy way of changing the admin password</li>
</ul>
</blockquote>
<blockquote class="tr_bq">
<ul>
<li>The user can now switch between image-tiling on the fly and using pre-tiling by means of a context menu (right-click onto the data set tree). </li>
</ul>
</blockquote>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL_M0ZTEs1VOOZW8vCTZbx_W0qkt6kOWl6IqfIezblzpiovDcSHZvweEiLc2aI0JcB_2mnnktK0q1E7zzG6v1NGyiaDrT1sQgNNQtE7_hcERLsIjTBoUFZursTt7DAr3ytS2e7uyQmd9-X/s1600/swap.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="317" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL_M0ZTEs1VOOZW8vCTZbx_W0qkt6kOWl6IqfIezblzpiovDcSHZvweEiLc2aI0JcB_2mnnktK0q1E7zzG6v1NGyiaDrT1sQgNNQtE7_hcERLsIjTBoUFZursTt7DAr3ytS2e7uyQmd9-X/s320/swap.png" width="320" /></a></div>
<div>
<br /></div>
<div>
<br /></div>
<div>
NOTE: Both features are restricted to the desktop version and not implemented in the mobile versions (yet).</div>
<div>
<br />
<br />
<br />
<strike>Binary Packages of version 1.2 can be downloaded here: <a href="http://caivm1.qern.qcif.edu.au/downloads/">http://caivm1.qern.qcif.edu.au/downloads/</a></strike></div>
<div>
<strike>or here: <a href="http://caivm2.qern.qcif.edu.au/downloads/">http://caivm2.qern.qcif.edu.au/downloads/</a> </strike></div>
<div>
<br /></div>
<div>
Newer Binaries can be found here:<br />
<br />
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a><br />
<br />
or<br />
<br />
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a></div>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-8517207284637395762013-06-18T15:21:00.003+10:002013-11-01T12:42:04.364+10:00Tissue Stack 1.1 - Binary PackagesThere are now binary packages available in .deb and .rpm format, all of them are for <u>64 bit</u> architectures only:<br />
<br />
<a href="http://caivm1.qern.qcif.edu.au/downloads/"><strike>http://caivm1.qern.qcif.edu.au/downloads/</strike></a><br />
<strike><a href="http://caivm2.qern.qcif.edu.au/downloads/">http://caivm2.qern.qcif.edu.au/downloads/</a></strike><br />
<br />
<b><u>UPDATE</u></b>: newer binaries can be found here:<br />
<br />
<a href="http://tissuestack.org/downloads/">http://tissuestack.org/downloads/</a><br />
<br />
or<br />
<br />
<a href="http://tissuestack.com/downloads/">http://tissuestack.com/downloads/</a><br />
<br />
The .deb package has been tested using Ubunbtu 11 and 12.<br />
The .rpm package has been tested on a Fedora 17 and 18 but should also work for CentOS.<br />
<br />
Ubuntu users will not need to install one of the major dependencies, the MINC library, whereas for Fedora and CentOS there is a pre-compiled rpm (64 bit) ready for download as well.<br />
<br />
<i><u>INSTALLATION INSTRUCTIONS:</u></i><br />
<i><u><br /></u></i>
<u>for .deb:</u><br />
<br />
<blockquote class="tr_bq">
Execute <i>sudo dpkg -i tissuestack_X.X_amd64.deb</i></blockquote>
This will very likely fail because of unsatisfied dependencies.<br />
<br />
<blockquote class="tr_bq">
Running <i>sudo apt-get install -f </i>should take care of installing the needed software for you.</blockquote>
<blockquote class="tr_bq">
After that rerun <i>sudo dpkg -i tissuestack_X.X_amd64.deb </i>again and it should complete without any errors.</blockquote>
Alternatively, using gdebi should also work in order to avoid the 3 step procedure above:<br />
<blockquote class="tr_bq">
<i>sudo gdebi dpkg -i tissuestack_X.X_amd64.deb</i></blockquote>
<br />
<u>for .rpm:</u><br />
<blockquote class="tr_bq">
Run <i>yum install minc-X.X-0.fc17.x86_64.rpm tissuestack-X.X-0.fc17.x86_64.rpm</i> as root/sudo</blockquote>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-29640161168360224332013-04-10T15:39:00.003+10:002013-04-11T14:40:31.714+10:00Announcing TissueStack<br />
<span style="font-family: Verdana, sans-serif;">TissueStack was originally designed for use in the 3D medical and scientific imaging field for data from 3D micro-CT, MRI and restacked histology data. The viewer has since been used for multiple datasets including museum specimens, coal mining samples and Electron Microscopy data.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif;">The original motivation for TissueStack came from the burgeoning size of micro-MRI and micro-CT datasets in scientific experiments. For a typical mouse brain imaging study this can amount to 12-15GB for a single scan. This problem is only exacerbated when re-stacked optical imaging (Histology) data is added to the analysis as these datasets can be up to 1TB in size. This presents a large barrier to collaborative research as it is difficult to share data between sites and keep collaborators up to date with the latest observations. What was needed was a 3D dataset viewing system that could be viewed remotely and had the ability to federate and overlay datasets from multiple sites, from these set of requirements TissueStack was born.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif;">So far, TissueStack has been used by researchers from UQ (Brisbane) and Curtin (Perth) to collaboratively annotate the highest resolution model of mouse anatomy to date as part of the AMBMC project. Without the abilities of TissueStack to link to specific parts of the data, efforts to identify sub-structures were reduced to lengthy conference calls in which the collaborators attempted to sync their views of the same data.</span><br />
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">From a technical standpoint, TissueStack is a web based HTML5 3D dataset viewer that generates image tiles on the fly, the main interface is shown below.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhB8vDbEzyuY_7Uu2KNLYYsp_gacn7nf7LA563_6Y00h1ECdqIAvbS7gxhu3YBdQir3AuPOcDSBhRXiECmE4x88aFYGleo2kxvJQL9veLICWXaFaDBvfFNXDzBY-AdA0tMwFfscHryzaA7p/s1600/main-interface-annot.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhB8vDbEzyuY_7Uu2KNLYYsp_gacn7nf7LA563_6Y00h1ECdqIAvbS7gxhu3YBdQir3AuPOcDSBhRXiECmE4x88aFYGleo2kxvJQL9veLICWXaFaDBvfFNXDzBY-AdA0tMwFfscHryzaA7p/s640/main-interface-annot.png" width="609" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The main TissueStack interface view</td></tr>
</tbody></table>
<span style="font-family: Verdana, sans-serif;">The viewer has been designed to mimic web based map viewing sites such that users can easily navigate. A demonstration of TissueStack can be seen here: <a href="http://caivm1.qern.qcif.edu.au/">http://caivm1.qern.qcif.edu.au/</a> There is also a mobile/tablet version of TissueStack with all the same functionality as the "desktop" version. The appropriate version of the site is loaded based upon the viewers current viewing platform.</span><br />
<br /></div>
<div>
<br /></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-58968003449948461992013-04-10T14:40:00.002+10:002013-04-10T15:44:27.840+10:00Testing methods and Findings<span style="font-family: Verdana, sans-serif;">Throughout its development TissueStack has had a group of four testers who have provided feedback. We have summarised the findings of this below and how it influenced our development path.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<h3>
<span style="font-family: Verdana, sans-serif;">Our Test Users</span></h3>
<div>
<span style="font-family: Verdana, sans-serif;"><b>User 1:</b> A researcher at Centre for Advanced Imaging with many years experience both using and writing image viewing software. We expected this user to have a knowledge of which features are most useful the largest number of users.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><b>User 2:</b> A Professor at the Montreal Neurological Institute with experience in image analysis and atlasing.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><b>User 3:</b> A Professor of anatomy and one of the authors of the most widely used paper based atlas of mouse neuroanatomy based in Perth and Sydney.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><b>User 4:</b> A post-doc at the Centre for Advanced Imaging with experience in atlas creation and manual brain segmentation.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<br />
<h3>
<span style="font-family: Verdana, sans-serif;">Common testing outcomes</span></h3>
<span style="font-family: Verdana, sans-serif;">Test users interacted with all parts of TissueStack excepting parts of the Administrative tab reserved for the upload of data. Given that the user interface has been modelled on the existing web paradigm of online mapping users were all able to rapidly navigate the datasets. Initial testing had users requesting features such as scale bars, dataset overlay, linking of datasets and progress indicators.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">These features were then added in subsequent releases and with some refinement are now all in the final release of TissueStack.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<br />
<h4>
<span style="font-family: Verdana, sans-serif;">Scale Bar/Indicator</span></h4>
<div>
<span style="font-family: Verdana, sans-serif;">Unbeknown to the developers this is a standard feature in nearly all histological datasets as it allows the user to gauge the current image with respect to others of possibly differing scales.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">A scale bar is typically not used in 3D MRI or CT data as the image typically covers the entire of the object. This obviously becomes important when viewing a high resolution MRI image in which the entire volume cannot always fit in a single view. As such we added a dynamic scale bar to the main TissueStack view, this bar changes as the user zooms in and out of the view.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<h4>
<span style="font-family: Verdana, sans-serif;">Dataset Overlay</span></h4>
<div>
<span style="font-family: Verdana, sans-serif;">A common request was for the ability to overlay two datasets, typically an MRI and optical imaging dataset or an MRI and a segmented image with regions of interest traced. The initial design of TissueStack meant that adding this feature was difficult as we had only planned for the simultaneous browsing of datasets (linked windows). As such a lot discussion regarding the best way to add this was generated in order to both satisfy the user feature request and to also preserve as much as we could of TissueStacks speed and flexibility. </span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">The feature was added in the final release of TissueStack but it does incur a small performance penalty. User testing of this feature has shown that the small speed drop is worth it for the added functionality. We have added extra functionality beyond the initial user request with an 'overlay control' that appears in the top left window when two datasets are displayed simultaneously.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">See this <a href="http://tissuestack.blogspot.com.au/2013/01/tissuestack-features-6.html">blog post</a> for more details on the implementation specifics.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<h4>
<span style="font-family: Verdana, sans-serif;">Linked Datasets</span></h4>
<div>
<span style="font-family: Verdana, sans-serif;">This feature was always planned from the beginning but user requests meant that we had to bring the timeline forward for its implementation ahead of colour mapping and links.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">This is probably one of the most used features of TissueStack as it allows the parallel browsing of linked datasets of differing scales. This was one of the primary aims of TissueStack. The link between the datasets is accomplished by storing a voxel to world transformation for all datasets in the TissueStack database.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">See this </span><a href="http://tissuestack.blogspot.com.au/2013/01/tissuestack-features-6.html" style="font-family: Verdana, sans-serif;">blog post</a><span style="font-family: Verdana, sans-serif;"> for more details on the implementation specifics</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<h4>
<span style="font-family: Verdana, sans-serif;">Progress Indicators</span></h4>
<div>
<span style="font-family: Verdana, sans-serif;">Users initially expressed some frustration in that TissueStack gave users no indicator of loading progress when rapidly navigating a dataset. This was especially apparent over slower connections and with larger datasets in which tiling performance is slower than user expectations.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">The best way to fix this problem is to speed up the tiling process itself by caching, pre-loading and using preview tiles at a lower resolution. This can be seen when panning around a dataset, in this case lower resolution images are loaded. These are then replaced by higher resolution images when navigation ceases. A tile queue culling algorithm was also implemented to speed rapid browsing.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;">After a significant amount of effort had been expended in speeding the tiling we went back to the users to gauge their response. The reply was that things were "much better" but still somewhat disorienting for new users. As such we implemented a progress indicator at the bottom centre that shows current drawing progress for the three tri-planar views.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<h3>
<span style="font-family: Verdana, sans-serif;">Individual User Experiences</span></h3>
<div>
<span style="font-family: Verdana, sans-serif;">Some issues were specific to our testing users needs for the software. We had to find a balance between their individual needs for extra functionality while keeping TissueStack as generic as possible while maintaining performance.</span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<div>
<span style="font-family: Verdana, sans-serif;"><b>User 1</b></span><br />
<span style="font-family: Verdana, sans-serif;">User 1 was strongly focussed on the ability to view and link data from multiple datasets, typically MRI, CT and Optical Microscopy. This is a large advantage TissueStack has over previous efforts in this area in which just the viewing needs of a single dataset are addressed.</span><br />
<br /></div>
<div>
<span style="font-family: Verdana, sans-serif;"><b>User 2</b></span><br />
<span style="font-family: Verdana, sans-serif;">User 2 was involved in early testing of TissueStack as it enabled us to test speed from a remote site (Canada). This user was initially impressed with the speed possible from a remote connection as compared to previous efforts he had seen and has remained so. This user primarily loads human neuroimaging data in TissueStack but has an interest in high resolution animal models.</span><br />
<br />
<span style="font-family: Verdana, sans-serif;"><b>User 3</b></span><br />
<span style="font-family: Verdana, sans-serif;">This user made extensive use of the links into datasets with geographically distant collaborators while annotating a high resolution mouse model. This feature was a large motivation for use of TissueStack and has meant a drive from paper to digital shared atlases in a number of associated projects.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif;"><b>User 4</b></span></div>
</div>
<div>
<span style="font-family: Verdana, sans-serif;">This user had many feature requests including online manual segmentation, collaborative viewing, scale bars, measurement tools, etc. These were driven by his own research and collaboration needs. Some of these features were implemented and some have been included in the future roadmap of TissueStack (online manual segmentation via SVG overlays). </span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-33234980502504752732013-02-27T11:19:00.001+10:002013-06-07T16:58:21.388+10:00Tissue Stack Installation<br />
<u>ATTENTION: This information is deprecated!</u><br />
<br />
<strike>So far Tisssue Stack had to be installed by compiling its source code and configuration by hand.</strike><br />
<strike><br /></strike>
<strike>Given that it consists of various parts written in C, Java and Java Script as well as its dependencies on an application server, web server and configuration database this task turns out to be more difficult than desired.</strike><br />
<strike><br /></strike>
<strike>The steps to do so are detailed in README files in the individual component's respective folder.</strike><br />
<strike><br /></strike>
<strike><b>HOWEVER</b>, there is now a binary install which will facilitate the above described procedure considerably although a few manual steps are still required to achieve a successful installation.</strike><br />
<strike><br /></strike>
<strike>Therefore, anybody who wants to merely install and use Tissue Stack, can do so by downloading the appropriate binary packages which can be found here:</strike><br />
<strike><br /></strike>
<a href="http://caivm1.qern.qcif.edu.au/downloads/"><strike>http://caivm1.qern.qcif.edu.au/downloads/</strike></a><br />
<strike>or:</strike><br />
<a href="http://caivm2.qern.qcif.edu.au/downloads/"><strike>http://caivm2.qern.qcif.edu.au/downloads/</strike></a><br />
<strike><br /></strike>
<strike>There is an INSTALL text file which will guide you through the process.</strike><br />
<strike><br /></strike>
<strike>Basically Tissue Stack was bundled into 2 parts:</strike><br />
<strike><br /></strike>
<strike>(1) Image Server (C code) => made available as a 64 bit Debian package</strike><br />
<strike>(2) Tissue Stack Web and Configuration Services => downloadable as a *.tar.gz</strike><br />
<strike><br /></strike>
<strike>Technically, either one can be installed without the other although this will result in limited functionality for (2). Essentially only manually pre-tiled and configured data sets can be displayed by (2) so it is recommended that you install both to take full advantage of the functionality available.</strike><br />
<strike><br /></strike>
<i><strike>Note:</strike></i><br />
<strike>Part (2) is a fairly large file (~100MB), a consequence of achieving ease of installation at the cost of a larger download. The archive contains a java runtime and tomcat installation as well as the compiled Tissue Stack Web Application itself. These would have to be installed individually otherwise and the resulting downloads would actually result in a bigger download altogether since build tools would have to be installed as well (maven)</strike><br />
<strike><br /></strike>
<i><strike>Potential Problems:</strike></i><br />
<strike>A) You do need super user privileges for some parts of the installation, e.g. debian package and postgresql database</strike><br />
<strike>B) Firewalls can prevent the installed system from working if they block ports 80 (apache), 5432 (postgresql) or 8080 (tomcat). Make sure you allow at least local access to the latter two, that's sufficient if access is proxied via the apache.</strike><br />
<strike>C) Configuration of the Apache Web Server: Make sure you have modules headers, proxy and proxy_http installed as well as the rules listed in the example configuration file that accompanies the installation archive.</strike><br />
<br />haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-20415730727359054332013-02-21T14:18:00.004+10:002013-02-21T14:20:16.706+10:00<br />
<br />
<h2>
<b><u><span style="color: #38761d; font-size: x-large;">Version 1.1</span></u></b></h2>
<span style="background-color: white; font-family: Arial, Helvetica, sans-serif; font-size: 15px;"><br /></span><span style="font-size: large;">
This is the latest version of Tissue Stack, fulfilling all of the project's functional requirements (the data-related ones aside).</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Like its previous versions it is available on github: <a href="http://github.com/NIF-au/TissueStack">http://github.com/NIF-au/TissueStack</a></span><br />
<br />
<br />
<blockquote class="tr_bq">
<span style="background-color: white; font-family: Arial, Helvetica, sans-serif;"><i>This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.</i></span></blockquote>
haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-2072830548592795892013-01-08T17:13:00.003+10:002013-01-08T17:13:55.289+10:00TissueStack Features - 8<span id="internal-source-marker_0.1374770097900182"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">TissueStack</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"> has a simple external query interface that allows other</span><span style="background-color: white; vertical-align: baseline;"> </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">applications and researchers to integrate the data in the application</span><span style="background-color: white; vertical-align: baseline;"> </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">to their own systems. </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">In order to achieve this, TissueStack supports embedding in other pages.</span></span><span style="color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;"> This version allows a user to embed a light version of Tissue Stack into any website with only few lines of code via the TissueStack web API.</span><br />
<span style="font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The screenshot below shows an example page with Tissue Stack embedded</span><b><img height="223" src="https://lh4.googleusercontent.com/TnMap-SpDZfKQuoDhIeV-riZUJgOBgbW6T-mK54owwTUaXeilYc3aaMMom0SP-FJhA2Vfn-cYxLAa9nB_wYYv-sEgTlbCBOz7PM0yaLjllEbwKGRyjc" width="400" /></b><br />
<span><b style="font-weight: normal;"><span style="font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"></span></b><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">The technical details for this are in a previous blog post <a href="http://tissuestack.blogspot.com.au/2012/07/embedding-tissue-stack.html">here</a>.</span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-80346088549349321612013-01-08T17:06:00.001+10:002013-01-08T17:06:08.080+10:00TissueStack Features - 7<span id="internal-source-marker_0.1374770097900182"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">TissueStack</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"> allows for data display from multiple sources running a TissueStack server</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"> via data federation. </span></span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;">This is achieved as the connection to a dataset on a client is via a socket connection to a TissueStack Server. This means that a single TissueStack Client can connect to multiple servers so long as they are internet accessible</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;">.</span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;">The interface for this is in the TissueStack Client via the "connect to Tissue Stack server” button on the left of the main image pane. All that is required is the corresponding URL of the server at which point the two instances datasets can be viewed.</span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;">The screenshot below shows a demonstration Tissue Stack instance connected to both a remote server and a server running on the localhost. This information is displayed in the list of available datasets.</span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;"><br /></span>
<span></span><br />
<div dir="ltr" style="font-weight: bold; margin-bottom: 0pt; margin-left: 45pt; margin-top: 0pt;">
<img height="417px;" src="https://lh3.googleusercontent.com/tahrkooC9X1uoTBIIPN9GvkKd76ScXvL14LvimZDuY5n_nDcdm6PcvoEqmCZKc2AtZygaIp-1cFXdfvd8Tni-ha1oL3Ei90tdREziw8u1sbbNyyeQ_8" width="293px;" /><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"></span></div>
<div style="font-weight: bold;">
<br /></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-44901751433814868122013-01-08T17:00:00.000+10:002013-01-08T17:01:25.633+10:00TissueStack Features - 6<b style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b>
<span id="internal-source-marker_0.1374770097900182"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">TissueStack</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"> permits the comparison of mutant vs. wildtype image data and will allow</span><span style="background-color: white; vertical-align: baseline;"> </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">for morphological investigation of differences between the two</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">.</span></span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The most common form of morphological comparison used for voxel data is to use either a combined view of both datasets or to overlay them. TissueStack supports both of these types of image comparison. As part of this the datasets are also synchronised via the inbuilt coordinate system (typically in mm).</span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">These two screenshots show the two styles of dataset synchronisation (side by side and overlay) In the case of the overlaid datasets, the second image has been set to use the Spectral colour map.</span></span><br />
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;"><br /></span></span>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8G3MSGYdZ8ORUv_-wLap4gndLFdDE79OgBcgo-ojTjhWz3XwDclaF1kPDcJADuxLkmm0M41I8uead2HF0gRsliz_oTqMg3fCNhCvObsZy-_6pZ_PQva0JhBuqTiGN16WsaOPiBZR7LHSX/s1600/sbs.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="343" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8G3MSGYdZ8ORUv_-wLap4gndLFdDE79OgBcgo-ojTjhWz3XwDclaF1kPDcJADuxLkmm0M41I8uead2HF0gRsliz_oTqMg3fCNhCvObsZy-_6pZ_PQva0JhBuqTiGN16WsaOPiBZR7LHSX/s400/sbs.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCvSh_CW-7M7PcdAZsI47H99XubSuqpdvrHgmaEmEBVWluNDIGT1VLEktd_pACwjlNX8S1hZsj0r0OJeI3qeHO_so-a0Hg2iPi5ARAzi-CyV5iXwlBkM1Po3O7n7W9fBGqiN88ejY7yS0C/s1600/overlay.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="343" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCvSh_CW-7M7PcdAZsI47H99XubSuqpdvrHgmaEmEBVWluNDIGT1VLEktd_pACwjlNX8S1hZsj0r0OJeI3qeHO_so-a0Hg2iPi5ARAzi-CyV5iXwlBkM1Po3O7n7W9fBGqiN88ejY7yS0C/s400/overlay.jpg" width="400" /></a></div>
<br />
<span style="font-family: Arial, Helvetica, sans-serif;">Control of the synchronisation and overlay is via the admin tab.</span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5dTFzrj8w0YLhyphenhyphen43NzHMzbtZmNbTljTe0HqfTpQSMAS0U3CNHFn-PUg0C1Pn486WXhjkflEb4JJ9preN-z2a9RcN54NVyJ8LYvn-oLR_r5xGG9GFSexDLKg4Hq7rfTLComZceLl4LSmMa/s1600/control.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="98" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5dTFzrj8w0YLhyphenhyphen43NzHMzbtZmNbTljTe0HqfTpQSMAS0U3CNHFn-PUg0C1Pn486WXhjkflEb4JJ9preN-z2a9RcN54NVyJ8LYvn-oLR_r5xGG9GFSexDLKg4Hq7rfTLComZceLl4LSmMa/s320/control.jpg" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: Arial, Helvetica, sans-serif;">When in overlay mode a new control is shown in the top left of the image pane, this controls the opacity of the overlaid image such that the image behind can be seen.</span></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIdTWJhAAjlVz298mBd8brNCWD9kU8YvSE4jX7PmM7lyAcAdEhbaH1FK0vP7RAiHkIQQ3PpyAB-P6S38Drj3NTfhBixATPFosCk4rfsshhSK93ih-ZDRZ6O-SCnUVmyRr01uVtb_JnOu7N/s1600/ovcontrol.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIdTWJhAAjlVz298mBd8brNCWD9kU8YvSE4jX7PmM7lyAcAdEhbaH1FK0vP7RAiHkIQQ3PpyAB-P6S38Drj3NTfhBixATPFosCk4rfsshhSK93ih-ZDRZ6O-SCnUVmyRr01uVtb_JnOu7N/s1600/ovcontrol.jpg" /></a></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-26787602933240908802013-01-07T13:20:00.002+10:002013-08-15T17:18:43.520+10:00TissueStack Features - 5<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">A design goal of TissueStack has always been to develop a system that c</span><b id="internal-source-marker_0.1374770097900182" style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">an be easily downloaded, installed and configured on a standard </span></b><b id="internal-source-marker_0.1374770097900182" style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">architecture by a relatively competent user for use at local sites.</span></b><br />
<b style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">In order to get the best possible performance using web technologies, a "TissueStack" install is comprised of 4 components. All of these components are in a single Github repository and can be downloaded using a simple </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">git clone from </span><span style="background-color: white; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><a href="https://github.com/NIF-au/TissueStack" style="color: #1155cc;">https://github.com/NIF-au/TissueStack</a><span style="color: #222222;"> or as a ZIP archive from this link: </span></span><span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;"><a href="https://github.com/NIF-au/TissueStack/archive/master.zip">https://github.com/NIF-au/TissueStack/archive/master.zip</a> </span></span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; white-space: pre-wrap;">An installation guide is provided for each part of TissueStack, these can be found on github, in the README for each component:</span><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The TissueStack Server (Coded in C):</span><br />
<br />
<a href="https://github.com/NIF-au/TissueStack/blob/master/src/c/README" style="font-family: Arial; font-size: 16px; white-space: pre-wrap;">https://github.com/NIF-au/TissueStack/blob/master/src/c/README</a><br />
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The TissueStack Server middle layer (Coded in Java):</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="background-color: white; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="color: #222222;"> </span><a href="https://github.com/NIF-au/TissueStack/blob/master/src/java/README" style="color: #1155cc;">https://github.com/NIF-au/TissueStack/blob/master/src/java/README</a></span></span><br />
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span>
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="vertical-align: baseline;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></span>
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="vertical-align: baseline;"><span style="font-family: Arial, Helvetica, sans-serif;">The TissueStack Server database (Postgres SQL): </span></span></span><br />
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span>
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="color: #1155cc; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"> <a href="https://github.com/NIF-au/TissueStack/blob/master/src/sql/README" style="font-size: medium; white-space: normal;">https://github.com/NIF-au/TissueStack/blob/master/src/sql/README</a></span></span></span><br />
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span>
<span style="background-color: white; color: #222222; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span>
<span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-size: 16px; white-space: pre-wrap;">The TissueStack Client web front end (that can be included in multiple websites for a single server): </span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="background-color: white; color: #1155cc; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"> <a href="https://github.com/NIF-au/TissueStack/blob/master/src/web/README">https://github.com/NIF-au/TissueStack/blob/master/src/web/README</a></span></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span id="internal-source-marker_0.1374770097900182"><span style="font-family: Arial, Helvetica, sans-serif;"></span></span><br />
<span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-size: 16px; white-space: pre-wrap;">In order to further ease the installation process, there exist binary packages: </span><br />
<span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-size: 16px; white-space: pre-wrap;"><br /></span>
<span style="background-color: white; color: #1155cc; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"> <a href="http://tissuestack.blogspot.com.au/2013/06/tissue-stack-11-binary-packages.html">http://tissuestack.blogspot.com.au/2013/06/tissue-stack-11-binary-packages.html</a></span></span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-57588310261235546412013-01-07T12:45:00.001+10:002013-01-07T12:45:06.019+10:00TissueStack Features - 4<span id="internal-source-marker_0.1374770097900182"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The TissueStack server </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">has a plugin architecture such that future modules for additional</span><span style="background-color: white; vertical-align: baseline;"> </span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">reference data can be added.</span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"> The client side code is all coded in HTML5 using standard methods and HTML elements, as such by its nature it is infinitely extensible and <a href="http://tissuestack.blogspot.com.au/2012/07/embedding-tissue-stack.html">embeddable</a>. </span><br /><b style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"></span></b><br /><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The plugin architecture API that is used on the server side of Tissue Stack is documented on github <a href="https://github.com/NIF-au/TissueStack/wiki/TissueStack-Server">here</a>. This mechanism allows external or future developers to implement and add new functionality. The plugin system also allows plugins to be included or removed without shutting down the server. Each plugin shares all data structures with the core server and can also interact with another plugins.</span></span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-44164211985947269872013-01-07T12:31:00.001+10:002013-01-07T12:32:51.949+10:00TissueStack Features - 3<b style="font-weight: normal;"><span style="background-color: #d9ead3; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b><span id="internal-source-marker_0.31207730807363987" style="background-color: white;"><span style="color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">TissueStack </span><span style="color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">has an interface to link additional anatomy metadata such as lobe</span><span style="vertical-align: baseline;"> </span><span style="color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">and structure names to the image data </span><span style="color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">being presented. This allows us to link labelled data and structure names to specific co-ordinates or areas. The eventual goal of this link is to allow the comparison of structures not only between two similar datasets but between species were there are homologous structures. A good example of this would be the hippocampal formation that exists in most higher order vertebrates. </span></span><br />
<b style="font-weight: normal;"><span style="background-color: #d9ead3; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b><b id="internal-source-marker_0.31207730807363987" style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">The screen shots below show how the current interface to this works, it is possible to associate a particular area of a dataset with a label, this label data is displayed when the co-ordinate centre is overlaid on an area. In both of these the label data can be seen in the top left corner, a label (“yellow (hot)”, “middle of brain (spectral)”) is associated with a specific colormap and dataset.</span></b><br />
<b style="font-weight: normal;"><span style="background-color: #d9ead3; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b>
<b id="internal-source-marker_0.31207730807363987" style="font-weight: normal;"><img height="148" src="https://lh4.googleusercontent.com/yZfSCRMJtUaXO9qqMkf1cQUUVNrFiG1rs0pj2XR25LSMnsGm-HQNXRpeZWLD9ZVgKnaJG1CRl0MORloQ2bdEYpONmI2SQJ5k9G5jvK8_FvgloJn1yAY" width="400" /></b><br />
<b style="font-weight: normal;"><br /></b>
<b id="internal-source-marker_0.31207730807363987" style="font-weight: normal;"><img height="97" src="https://lh6.googleusercontent.com/6QunNnj4w-_IUjWQGWfbjxr6eXpU1w_isFBZuZE2d7JQI1trz4WW87WV2_qhhSlD8jEcPpvJvzS8RKy_gRt_e1nZ7Fp40IOQo01JSlOB_I8bqmYGsxY" width="400" /></b>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-64351318737623151312012-12-21T16:12:00.001+10:002012-12-21T16:12:14.118+10:00TissueStack Features - 2<span id="internal-source-marker_0.7394757741130888"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">TissueStack will now also <b>display appropriate meta-data from both microscopy (histology) and</b></span><span style="background-color: white; vertical-align: baseline;"><b> </b></span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><b>MRI fields </b>along with datasets. This feature displays the common co-ordinate data between two datasets that are used to link them in the "world space". Here, world space refers to a millimetric co-ordinate reference frame in which all datasets must reside. </span></span><br />
<span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">Shown below are the real world (mm) co-ordinates for both the whole volume (bounding box) and the current point of interest. The current scale being used to view the dataset, the value of the current point of interest (in gray) and the scale of the data overlaid on the main viewing pane.</span></span><br />
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;"><br /></span></span>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">This pane will display more meta-data from the datasets as it becomes available, specifically data from the XML RIF-CS data feed will also be displayed.</span></span><br />
<span><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span>
<div class="separator" style="clear: both; text-align: center;">
<b id="internal-source-marker_0.7394757741130888" style="font-weight: normal; margin-left: 1em; margin-right: 1em;"><img height="222" src="https://lh3.googleusercontent.com/yPGlHe1L3TpzkagoOJY5DeDG-32pwmKEybsm6Kc6C27yVVcvYkVNpS4t8QENQQAWJm4WauH0kUHzqnX6yytWFnWTCZEpxfruMqwGf-pO8KQuoS2uJuQ" width="400" /></b></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-88466170246565858192012-12-21T16:03:00.000+10:002012-12-21T16:03:50.428+10:00TissueStack Features - 1<div>
<span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">The original description of TissueStack called for a number of features the first of these was for the </span></span><b id="internal-source-marker_0.7394757741130888" style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">interactive combined or adjacent display of multi-scale </span></b><b id="internal-source-marker_0.7394757741130888" style="font-weight: normal;"><span style="background-color: white; color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">MRI, histology, nomenclature data an</span><span style="background-color: white;"><span style="color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;">d</span><span style="color: #222222; font-family: Arial; font-size: 16px; font-weight: bold; vertical-align: baseline; white-space: pre-wrap;"> corresponding project metadata</span><span style="color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;">.</span></span></b></div>
<div>
<b style="font-weight: normal;"><span style="background-color: white;"><span style="color: #222222; font-family: Arial; font-size: 16px; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></b></div>
<div>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">With recent developments we can now announce that we have met this goal, the current release of TissueStack now allows you to display 2 datasets beside each other. These datasets can be of any modality as the only input requirement is a file in either NiFTI or MINC format. Nomenclature and metadata (co-ordinates, colormaps) are displayed in the left pane. The most important of this the co-ordinate system as it is by this common reference frame that images are linked.</span></span></div>
<div>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;"><br /></span></span></div>
<div>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;">An example screenshot of this is shown below. In this case a restacked histology is shown in the top panel and the corresponding MRI from the same animal is shown in the bottom panel</span></span></div>
<div>
<span style="color: #222222; font-family: Arial;"><span style="white-space: pre-wrap;"><br /></span></span></div>
<div>
<div class="separator" style="clear: both; text-align: center;">
<b id="internal-source-marker_0.7394757741130888" style="font-weight: normal; margin-left: 1em; margin-right: 1em;"><img height="210" src="https://lh4.googleusercontent.com/qEcPg44-2tIwFmoWTJrzj-_lCBzfPVZvjPOYPrl3G0fyGZM9B3NIc92Mn44ujUx1IQ24apEnqz2Zgw16wm75ufrC1T_znp--ugnvZb3FihOht_9IbTU" width="400" /></b></div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-84350623240436532152012-11-26T15:44:00.003+10:002012-11-26T15:46:43.272+10:00Pixel Values: Lookup FilesThe development branch of TissueStack now contains code to allow a text/label look-up by grayscale value/RGB triple defined in a file of the following layout:<br />
<br />
<blockquote class="tr_bq">
0<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>Black (Background)<br />
1<span class="Apple-tab-span" style="white-space: pre;"> </span>197<span class="Apple-tab-span" style="white-space: pre;"> </span>197<span class="Apple-tab-span" style="white-space: pre;"> </span>99<span class="Apple-tab-span" style="white-space: pre;"> </span>yellow (hot)<br />
2<span class="Apple-tab-span" style="white-space: pre;"> </span>170<span class="Apple-tab-span" style="white-space: pre;"> </span>170<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>middle of brain (spectral)<br />
3<span class="Apple-tab-span" style="white-space: pre;"> </span>167<span class="Apple-tab-span" style="white-space: pre;"> </span>167<span class="Apple-tab-span" style="white-space: pre;"> </span>0<span class="Apple-tab-span" style="white-space: pre;"> </span>Center</blockquote>
<div>
<u><i>Notes: </i></u></div>
<ul>
<li>The number of required columns has to be 5 where the leading one is an at the moment unused number increment and the last column contains the associated text/label</li>
<li>The separator has to be tabs!</li>
<li>For gray-scale look-ups just set column 2 - 4 (RGB) to the desired gray-scale value</li>
</ul>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjF6G0Vgpyd28GNQ7LXLiPYB3alSJJWKBmLzGJ5SkHNPgnGGRli6-LwiaE_UFtZt4qhAHGEVkh3kz5TqK7mnUlrDKTTBQcooDKbNacUyXzC_sZng07lkJK0sTF-HAARbIvSscZpyJ28DzBP/s1600/lookup.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="91" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjF6G0Vgpyd28GNQ7LXLiPYB3alSJJWKBmLzGJ5SkHNPgnGGRli6-LwiaE_UFtZt4qhAHGEVkh3kz5TqK7mnUlrDKTTBQcooDKbNacUyXzC_sZng07lkJK0sTF-HAARbIvSscZpyJ28DzBP/s320/lookup.png" width="320" /></a></div>
<br />haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-6822887763463238732012-11-19T18:07:00.001+10:002012-11-19T18:09:34.112+10:00Version 0.9 (GPL3)TissueStacks' version 0.9 source code is now available under the <i style="text-decoration: underline;">GNU General Public License</i> (Version 3).<br />
<br />
<div style="text-align: center;">
***</div>
<br />
The main feature of this version is the <b><u>overlay of 2 data sets</u></b> in the desktop version of the software:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIRXgieHNw-2yY6gUP-Uf2o_QpAxUHOgHH3zPiUNOWAmt01g6ZrotEZeK-6LrSrxEhWecYeGGIItqATtqdYeL4X88c935D4knNN3p_CFp_LKrs3w2S-YJSAB1gAK-ffquYJXr8MHowxNNd/s1600/overlay.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="234" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIRXgieHNw-2yY6gUP-Uf2o_QpAxUHOgHH3zPiUNOWAmt01g6ZrotEZeK-6LrSrxEhWecYeGGIItqATtqdYeL4X88c935D4knNN3p_CFp_LKrs3w2S-YJSAB1gAK-ffquYJXr8MHowxNNd/s320/overlay.png" width="320" /></a></div>
<br />
To enable overlay viewing, simply go into the ADMIN tab and select the appropriate option, then select the two data sets to compare.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgt8YrqrofzeC648IchhiDf8wczg99PRccMLyv5xzFhus2ietId1jT7-mloWP-SG0RYM8uX7KnzimlLQCISY2jGAymLkAQFHEOO1J3keM0Y1qA2fTDN2uZLbSQR2rMtAEhFgZJFk1lHOJLI/s1600/settings.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="107" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgt8YrqrofzeC648IchhiDf8wczg99PRccMLyv5xzFhus2ietId1jT7-mloWP-SG0RYM8uX7KnzimlLQCISY2jGAymLkAQFHEOO1J3keM0Y1qA2fTDN2uZLbSQR2rMtAEhFgZJFk1lHOJLI/s320/settings.png" width="320" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<u><i>Notes:</i></u><br />
<ul>
<li>If only option "Synchronize Data Sets" is checked, both data sets are displayed, the first on top, the second beneath. When navigating within either one of the two, the other will "follow"</li>
<li>The "natural" order of the overlay is such that, out of 2 selected data sets, the one that comes first in the tree view will be below, the second on top.</li>
</ul>
<br />
Additionally, the transparency wheel enables the user to control the transparency of the top data set, the swap icon exchanges the order of the overlay:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAQpysxg-z4H0ymxvWQWHvXef1lOn7aRMP_2UapCzTQ-fmgW7o6ZvkoOjE_TTOFksKZzM-xpSDn324fSrIgPwFTS_8rPvEJvWPJrudsDfuzGKnvSMlhUXjPSDSNJB2UUeR6kf_koSqcHsT/s1600/options.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="34" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAQpysxg-z4H0ymxvWQWHvXef1lOn7aRMP_2UapCzTQ-fmgW7o6ZvkoOjE_TTOFksKZzM-xpSDn324fSrIgPwFTS_8rPvEJvWPJrudsDfuzGKnvSMlhUXjPSDSNJB2UUeR6kf_koSqcHsT/s320/options.png" width="320" /></a></div>
<br />
Besides the overlay feature, TissueStack now reads the color maps (more flexibly) from a directory, provided they follow a simple 4 column structure, separated by a space e.g:<br />
<blockquote class="tr_bq">
0.0 0.0 0.0 0.0<br />
1.0 0.0 1.0 0.0</blockquote>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjv6W-F8O80dAnXIKsKyjTRcTX38OvskuEtFTdHiT-IUKrtVY_-CnomkWiTsz6Jwq5IBYZRzmTIttChJFRGSG82lQdCJYMv83at8dRa29P2iysDrWoNAYV2dvZkI-GHNnFrU699MHnZgu6_/s1600/colormap.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjv6W-F8O80dAnXIKsKyjTRcTX38OvskuEtFTdHiT-IUKrtVY_-CnomkWiTsz6Jwq5IBYZRzmTIttChJFRGSG82lQdCJYMv83at8dRa29P2iysDrWoNAYV2dvZkI-GHNnFrU699MHnZgu6_/s320/colormap.png" width="320" /></a></div>
<br />
<br />
<br />haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0tag:blogger.com,1999:blog-1594281488726050150.post-85276338132962330662012-11-08T18:04:00.000+10:002012-11-08T18:12:32.876+10:00Functionality Update<b><i><u>Task Management</u></i></b><br />
<br />
As promised in the previous blog post Tissue Stack can now do image format conversions and pre-tiling more conveniently through the user interface:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyn7soqSZBQpp4H8XRNCyq6EaRSH_IhJkMaHBF28Nfh1LI8U9TlqxmXdI60pJL7lKftDj22qgLDREjYcAIgM7-9WsqcD_4zU9q6wgZ0fNL17OTbmCAD2k4YUp7ml2970T7wC1RhbYa-tQV/s1600/admin_options.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="165" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyn7soqSZBQpp4H8XRNCyq6EaRSH_IhJkMaHBF28Nfh1LI8U9TlqxmXdI60pJL7lKftDj22qgLDREjYcAIgM7-9WsqcD_4zU9q6wgZ0fNL17OTbmCAD2k4YUp7ml2970T7wC1RhbYa-tQV/s320/admin_options.png" width="320" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwC0U-SAHIc-SN9ePDwLVu85qE-AsrtaS-ij_2qqLvsXkDUiZwfbkQmrpROof1vV-PibHzBgXntr9l_ihOi72Z85QTH1q4VrINXetEJfcTpXp-AW_NJKSdRZ9sz-DKHqMP_co1Yd4jht5V/s1600/tasks_status.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="47" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwC0U-SAHIc-SN9ePDwLVu85qE-AsrtaS-ij_2qqLvsXkDUiZwfbkQmrpROof1vV-PibHzBgXntr9l_ihOi72Z85QTH1q4VrINXetEJfcTpXp-AW_NJKSdRZ9sz-DKHqMP_co1Yd4jht5V/s320/tasks_status.png" width="320" /></a></div>
<br />
Any of the given options above operate on source files in the upload directory only.<br />
As mentioned before the formats supported are Nifti and Minc 2.<br />
<br />
It's worth noting that Nifti and Minc 2 inputs have to be converted to our internal "raw" format prior to adding them to the local instance's configuration (as displayed in the "Data" tab tree on the left panel), otherwise you'll get a corresponding pop-up that tells you exactly that ;-)<br />
<br />
<b><i><u>Data Set Value Display</u></i></b><br />
<b><i><u><br /></u></i></b>
So far only the coordinates were displayed for the point that marks the cross-hair position. Now there is an additional field in the UI that gives you the underlying value as a single figure or an rgb triple in case you have a color map applied:<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-f5AooCVjxRE7g8mRbJTAgojPmMbgIG_2nGh9MpYNkQySFNe3h-tM32ilyMSPSWv6PwU_PEIpFoAdzm5fGct_5aKFNmg2fJ5KOp0AYsHEVCfiP-uHolog2GfY0hpNQ0o-N8nqscwIEyZV/s1600/value.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-f5AooCVjxRE7g8mRbJTAgojPmMbgIG_2nGh9MpYNkQySFNe3h-tM32ilyMSPSWv6PwU_PEIpFoAdzm5fGct_5aKFNmg2fJ5KOp0AYsHEVCfiP-uHolog2GfY0hpNQ0o-N8nqscwIEyZV/s1600/value.png" /></a></div>
<br />
<br />
If the uploaded file had an original value range that was different from the 256 gray scale values, the canvas pixel value will get mapped back to that original range so that the original value can be displayed.<br />
<br />
<b><i><u>Upcoming Features:</u></i></b><br />
<b><i><u><br /></u></i></b>
1) Display of look-up values for Data Set pixels: Given a look-up table, the text field that for now only displays the underlying pixel's value will also give you the string associated in the look-up table.<br />
<br />
2) Import and display of RGB data sets<br />
<br />
3) ANDS data set registration: Optionally, if you add a data set to the configuration, meta-information will be stored in an xml which can then be harvested by ANDS => <a href="http://ands.org.au/">http://ands.org.au/</a><br />
<br />
<br />haraldhttp://www.blogger.com/profile/16339927500308467334noreply@blogger.com0