Changes between Version 3 and Version 4 of Optical

Timestamp:

Apr 30, 2014, 6:47:23 PM (11 years ago)

Author:

Tom Goddard

Comment:

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Optical

@@ -13 +13 @@
 5. Chimera 1 used to be able to display multi-channel image data in the Volume Viewer tool, developed for looking at fluorescently labeled chromosomes with John Sedat.  That capability was removed around 2008 because it add a great deal of complexity to the user interface code and was seldom used.  Multi-channel data can be displayed in current Chimera but with grayscale ("solid" style) rendering it does not blend the colors from the different channels.  This is because Chimera in general does not correctly display 2 transparent models.  While surface rendering works correctly for multichannel image data treating each channel as a separate map, surfaces often are not suitable for optical data because the intensity level varies such that there are interesting features at different levels that need to be shown simultaneously. In theory Chimera could blend the colors in grayscale mode for maps with identical grids without any change to user interfaces.  This code would be moderately complex because it involves rendering multiple models as a single group contrary to the Chimera rendering paradigm where each model is rendered independently.
 
-6. Optical microscopy, including the many super-resolution techniques is too low resolution to be compared directly to molecular structures -- the core capability of Chimera.  So adding optical microscopy capabilities would not benefit from the molecular analysis capabilities except to the extent that the same researchers also are interested in molecular structure and they could use the same software for both.  The same criticism applies to serial milling electron microscopy techniques (focused ion beam SEM, and serial block face SEM), data we do try to handle since the electron microscopy Chimera user base also uses those EM techniques.
+6. Optical microscopy, including the many super-resolution techniques, has too low resolution to be compared directly to molecular structures -- the core capability of Chimera.  So adding optical microscopy capabilities would not benefit from the molecular analysis capabilities except to the extent that the same researchers also are interested in molecular structure and they could use the same software for both.  The same criticism applies to serial milling electron microscopy techniques (focused ion beam SEM, and serial block face SEM), data we do try to handle since the electron microscopy Chimera user base also uses those EM techniques.
 
 7. An enticing reason for developing optical microscopy analysis software is that 3d optical imaging is producing exciting data (e.g. brain imaging), the emerging microscope technology is rapidly improving and software to support it seems not to have been developed.