Changeset 186:1770630d1c3e


Ignore:
Timestamp:
03/28/2012 04:40:27 PM (6 years ago)
Author:
Dmitry Fedorov <fedorov@…>
Branch:
default
Phase:
public
Message:

updates docs

Location:
bioView3D
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • bioView3D/LICENCE.txt

    r122 r186  
    11bioView3D
    22
    3 Copyright © 2008-2010 Center for Bio-Image Informatics, UCSB
     3Copyright © 2008-2012 Center for Bio-Image Informatics, UCSB
    44<http://www.bioimage.ucsb.edu/>
    55
  • bioView3D/bioview3d.pro

    r176 r186  
    2525# configuration: editable
    2626#---------------------------------------------------------------------
    27 VERSION = 0.1.15
     27VERSION = 0.1.17
    2828
    2929CONFIG += release
  • bioView3D/changelog.txt

    r179 r186  
    11= Version Change Log =
     2
     3== 0.1.17 ==
     4       
     5 * NEW: time projections for gobjects
     6 * IMPROVED: much improved support for 4D images: rendering speed, caching
     7 * IMPROVED: improved gobjects rendering
     8 * IMPROVED: several small UI changes
     9 * FIXED: OIB reader fixed for large files
     10 * FIXED: Bisque access fixed for the new database
    211
    312== 0.1.15 ==
  • bioView3D/doc/bioview3d.html

    r178 r186  
    1717
    1818<div class="pagebody">
    19   <p>bioView3D volume renderer is an open source and cross-platform application intended for bio-scientists to visualize fluorescence imagery in 3D. It supports images with up to 5 dimensions (3D + time + channels). bioView3D runs on Windows, MacOS X and Linux. It's based on OpenGL and will run smooth on modern hardware. bioView3D supports popular image stack formats like TIFF, Olympus Fluoview, Olympus OIB, Zeiss LSM, Zeiss ZVI, OME-TIFF, BioRad PIC, etc.</p>
     19  <p>bioView3D volume renderer is an open source and cross-platform application intended for bio-scientists to visualize fluorescence imagery in 3D. It supports images with up to 5 dimensions (3D + time + channels). bioView3D runs on Windows, MacOS X and Linux. It's based on OpenGL and will run smooth on modern hardware. bioView3D supports popular image stack formats like TIFF, Olympus Fluoview TIFF, Olympus OIB, Zeiss LSM, Zeiss ZVI, OME-TIFF, BioRad PIC, etc.</p>
    2020  <p>bioView3D has all the necessary tools embedded - image interpolation and channel remapping, it can show up to 7 simultaneous channels. The volume  is constructed using meta-data extracted from image files so it's physically accurate and seamless to users. It's also possible to export 3D images, screens and videos into files.</p>
    2121  <ul>
     
    2323    <li><strong>Minimum recommended  platform</strong>: Intel Core2Duo, 2GB RAM, nVidia 7x series</li>
    2424    <li><strong>Suggested  hardware</strong>: 4GB RAM (more is better), 512MB video memory  (more is better)</li>
     25    <li><strong>Limitations</strong>: Does not load multi-file images, see <a href="#MULTI_FILE">loading multi-file images</a></li>   
    2526  </ul>
    2627 
    27  
     28  <p>External links:</p>
     29  <ul>
     30    <li><a href="http://www.bioimage.ucsb.edu/downloads/BioView3D">Main web page</a></li>
     31    <li><a href="http://biodev.ece.ucsb.edu/projects/awall/wiki/BioView3D/Changelog">Change log</a></li>
     32    <li><a href="http://biodev.ece.ucsb.edu/projects/bioimage/downloader/download/category/5">Downloads</a></li>
     33  </ul>
    2834  <div class="contentsindex">
    29   <h3>Contents</h3>
     35    <h3>Contents</h3>
    3036  <ul>
    3137    <li><a href="#FEATURES">Features</a></li> 
     
    3945   
    4046        <li><a href="#TUTORIALS">Video tutorials</a></li>
    41         <li class="indent1"><a href="#VIDEO_SIMPLE">First look</a></li>
    42         <li class="indent1"><a href="#VIDEO_AUTO_ROTATION">Auto rotation</a></li>           
    43     <li class="indent1"><a href="#VIDEO_4D">Navigation in images with time</a></li>
    44         <li class="indent1"><a href="#VIDEO_GOBS">Graphical annotations</a></li>
    45     <li class="indent1"><a href="#VIDEO_BISQUE">Import images and annotations from Bisque web database</a></li>
    46    
    47     <li class="indent1"><a href="#VIDEO_EXPORT">Export of video</a></li>       
    48     <li class="indent1"><a href="#VIDEO_EXPORT_LIVE">Export of live video</a></li>   
     47          <li class="indent1"><a href="#TUTORIALS">First look</a></li> 
     48          <li class="indent1"><a href="#TUTORIALS">Auto rotation</a></li>           
     49      <li class="indent1"><a href="#TUTORIALS">Navigation in images with time</a></li>
     50          <li class="indent1"><a href="#TUTORIALS">Graphical annotations</a></li>
     51    <li class="indent1"><a href="#TUTORIALS">Import images and annotations from Bisque web database</a></li>
     52    <li class="indent1"><a href="#TUTORIALS">Export of video</a></li>           
     53    <li class="indent1"><a href="#TUTORIALS">Export of live video</a></li>   
    4954 
     55        <li><a href="#MULTI_FILE">Loading multi-file images</a></li>
     56
    5057        <li><a href="#SAMPLES">Sample datasets</a></li>
    51         <li class="indent1"><a href="#SAMPLES_3D">3D dataset</a></li>   
     58        <li class="indent1"><a href="#SAMPLES_3D">3D dataset</a></li>   
    5259    <li class="indent1"><a href="#SAMPLES_4D">4D dataset</a></li>   
    5360   
     
    114121 
    115122  <h3><a name="TUTORIALS" id="TUTORIALS"></a>Video tutorials</h3> 
    116  
    117   <h4><a name="VIDEO_SIMPLE" id="VIDEO_SIMPLE"></a>First look</h4>
    118   <div id='player_sample_1'>Your need flash player to display this video.</div>
     123
     124  <div id='player_sample'>Your need flash player to display this video.</div>
    119125  <script type='text/javascript'>
    120     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
     126    var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','900','370','9','#000000');
    121127    so.addParam('allowfullscreen','true');
    122128    so.addParam('allowscriptaccess','always');
    123129    so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    124     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_first_look.m4v'); 
    125     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_first_look.jpg');
    126     so.write('player_sample_1');
    127   </script>
    128 
    129   <h4><a name="VIDEO_AUTO_ROTATION" id="VIDEO_AUTO_ROTATION"></a>Auto rotation</h4>
    130   <div id='player_sample_1a'>Your need flash player to display this video.</div>
    131   <script type='text/javascript'>
    132     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    133     so.addParam('allowfullscreen','true');
    134     so.addParam('allowscriptaccess','always');
    135     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    136     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_auto-rotation.m4v'); 
    137     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_auto-rotation.jpg');
    138     so.write('player_sample_1a');
     130    so.addVariable('playlistfile','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_tutorials.xml'); 
     131    so.addVariable('playlist','left');   
     132    so.addVariable('playlistsize','300');       
     133    so.write('player_sample');
    139134  </script>
    140135 
    141   <h4><a name="VIDEO_4D" id="VIDEO_4D"></a>Navigation in images with time</h4>
    142  
    143   <div id='player_sample_2'>Your need flash player to display this video.</div>
    144   <script type='text/javascript'>
    145     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    146     so.addParam('allowfullscreen','true');
    147     so.addParam('allowscriptaccess','always');
    148     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    149     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_images_with_time.m4v'); 
    150     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_images_with_time.jpg');
    151     so.write('player_sample_2');
    152   </script> 
    153  
    154    
    155   <h4><a name="VIDEO_GOBS" id="VIDEO_GOBS"></a>Graphical annotations</h4>
    156  
    157   <div id='player_sample_3'>Your need flash player to display this video.</div>
    158   <script type='text/javascript'>
    159     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    160     so.addParam('allowfullscreen','true');
    161     so.addParam('allowscriptaccess','always');
    162     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    163     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_graphical_annotations.m4v'); 
    164     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_graphical_annotations.jpg');
    165     so.write('player_sample_3');
    166   </script>   
    167  
    168  
    169   <h4><a name="VIDEO_BISQUE" id="VIDEO_BISQUE"></a>Import images and annotations from Bisque web database</h4> 
    170  
    171   <div id='player_sample_4'>Your need flash player to display this video.</div>
    172   <script type='text/javascript'>
    173     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    174     so.addParam('allowfullscreen','true');
    175     so.addParam('allowscriptaccess','always');
    176     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    177     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_import_from_bisque.m4v'); 
    178     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_import_from_bisque.jpg');
    179     so.write('player_sample_4');
    180   </script>   
    181  
    182   <h4><a name="VIDEO_EXPORT" id="VIDEO_EXPORT"></a>Export of video</h4> 
    183  
    184   <div id='player_sample_5'>Your need flash player to display this video.</div>
    185   <script type='text/javascript'>
    186     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    187     so.addParam('allowfullscreen','true');
    188     so.addParam('allowscriptaccess','always');
    189     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    190     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_video_export.m4v'); 
    191     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_video_export.jpg');
    192     so.write('player_sample_5');
    193   </script>   
    194  
    195   <h4><a name="VIDEO_EXPORT_LIVE" id="VIDEO_EXPORT_LIVE"></a>Export of live video</h4> 
    196  
    197   <div id='player_sample_6'>Your need flash player to display this video.</div>
    198   <script type='text/javascript'>
    199     var so = new SWFObject('http://www.bioimage.ucsb.edu/software/bioView3D/flash/player5.2.swf','ply','600','370','9','#000000');
    200     so.addParam('allowfullscreen','true');
    201     so.addParam('allowscriptaccess','always');
    202     so.addVariable('skin','http://www.bioimage.ucsb.edu/software/bioView3D/flash/skins/stylish.swf');
    203     so.addVariable('file','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_video_live_export.m4v'); 
    204     so.addVariable('image','http://www.bioimage.ucsb.edu/software/bioView3D/videos/bioview3d_video_live_export.jpg');
    205     so.write('player_sample_6');
    206   </script>     
     136
     137 <h3><a name="MULTI_FILE" id="MULTI_FILE"></a>Loading multi-file images</h3>
     138 <p>bioView3D does not load multi-file images for the reason that most modern microscopes produce single file 5D images that contain all the necessary image data and metadata. Although it is possible to construct a single 5D image file from multiple files using <a href="http://www.bioimage.ucsb.edu/downloads/BioImage%20Convert">BioImage Convert</a> utility. It is available for Windows, MacOSX and Linux and supports many image formats. I could suggest to create images in OME-TIFF image format for it is an open and widely supported format, it is a normal multi-page TIFF file containing an XML description of image geometry in the description tag. The following command line would construct a 3D Z stack from 3 input images with resolution of X 0.2um Y 0.2um Z 1.0um T 1.0s:</p>
     139 <pre>imgcnv -i in1.tif -i in2.tif -i in3.tif -o out.ome.tif -t ome-tiff -geometry 3,1 -resolution 0.2,0.2,1.0,1.0</pre>   
    207140 
    208141 
    209142 <h3><a name="SAMPLES" id="SAMPLES"></a>Sample datasets</h3>
    210143 
    211  <a href="http://dough.ece.ucsb.edu/bisquik/browser?tag_query=&quot;bioView3D-examples&quot;">Example datasets</a> are accessible via the Bisque database. Images are stored along their textual and graphical annotations and can be viewed using the web browser or by downloading original data. Use the following URL to browse available example images: <a href="http://dough.ece.ucsb.edu/bisquik/browser?tag_query=&quot;bioView3D-examples&quot;">http://dough.ece.ucsb.edu/bisquik/browser?tag_query=&quot;bioView3D-examples&quot;</a>. Double-click in order to open a detailed image view. Once in the image view you can download the image by using the &quot;Download menu&quot;.
     144 <a href="http://bisque.ece.ucsb.edu/client_service/view?resource=http://bisque.ece.ucsb.edu/data_service/dataset/1930977">Example datasets</a> are accessible via the Bisque database. Images are stored along their textual and graphical annotations and can be viewed using the web browser or by downloading original data. Click in order to open a detailed image view. Once in the image view you can download the image by using the &quot;Download&quot; menu or start bioView3D if properly installed using &quot;External&quot; menu.
    212145 <h4><a name="SAMPLES_3D" id="SAMPLES_3D"></a>3D dataset - Fixed rabbit retina</h4>
    213  <p>The first image shows 
    214 fixed rabbit retina cross-section,  done at the Fisher Laboratory at UCSB using an
    215    Olympus FV-500 laser scanning confocal microscope. The sample is
     146 <p>The first image shows fixed rabbit retina cross-section,  acquired  using an
     147   Olympus FV-500 laser scanning confocal microscope and a courtesy of Geoff Lewis and the Fisher's Laboratory at MCDB, UCSB. The sample is
    216148   stained with <strong>GFAP: Cy5</strong> (Labels glial cells), <strong>BrdU : Cy3</strong> (Stain incorporated into dividing cells going
    217149  through S-phase (DNA synthesis) at time of administration), <strong>Mib-1: Cy2</strong> (Labels dividing cells in all   phases). The physical image dimensions are 127x127x12.6 microns (512x512x51 voxels) and the voxel size  is 0.248592x0.248592x1.0 microns. Image format: Olympus Fluoview TIFF.</p>
    218  <p>Browse: [<a href="http://dough.ece.ucsb.edu/bisquik/view?resource=http://dough.ece.ucsb.edu/ds/images/818025">using web browser</a>]<br />
    219   Download: [<a href="http://dough.ece.ucsb.edu/imgsrv/34943">Original image</a>], [<a href="http://dough.ece.ucsb.edu/ds/images/818025/gobjects?view=deep,canonical">Associated graphical annotations</a>]
     150 <p>Browse: [<a href="http://bisque.ece.ucsb.edu/client_service/view?resource=http://bisque.ece.ucsb.edu/data_service/image/818025">using web browser</a>]<br />
     151  Download: [<a href="http://bisque.ece.ucsb.edu/image_service/images/ad3d0326e45add97b676df43b3f5334601665453">Original image</a>], [<a href="http://bisque.ece.ucsb.edu/data_service/image/818025/gobject?view=deep,canonical">Associated graphical annotations</a>]
    220152 </p>
    221153
    222154
    223155 <h4><a name="SAMPLES_4D" id="SAMPLES_4D"></a>4D dataset - Cell mitosis</h4>
    224  <p>This 4D image shows  mitosis (cell division) stages  Metaphase-Anaphase by fluorescent tagging of mitotic spindles. The physical image dimensions are 45.9x45.9x12.9 microns (256x256x14 voxels) with 68 time ponits and the voxel size  is 0.179297x0.179297x0.928571 microns. Image format: Olympus OIB.</p>
    225  <p>Browse: [<a href="http://dough.ece.ucsb.edu/bisquik/view?resource=http://dough.ece.ucsb.edu/ds/images/818010">using web browser</a>]<br />
    226   Download: [<a href="http://dough.ece.ucsb.edu/imgsrv/34941">Original image</a>]
     156 <p>This 4D image shows  mitosis (cell division) stages  Metaphase-Anaphase by fluorescent tagging of mitotic spindles, courtesy of Alphan Altinok, Caltech. The physical image dimensions are 45.9x45.9x12.9 microns (256x256x14 voxels) with 68 time ponits and the voxel size  is 0.179297x0.179297x0.928571 microns. Image format: Olympus OIB.</p>
     157 <p>Browse: [<a href="http://bisque.ece.ucsb.edu/client_service/view?resource=http://bisque.ece.ucsb.edu/data_service/image/818010">using web browser</a>]<br />
     158  Download: [<a href="http://bisque.ece.ucsb.edu/image_service/images/1ec5c3319ae2191a3f83d632982b0f44fd624c07">Original image</a>]
    227159 </p>
    228160 
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