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EM3D 2.0 Full Release 1

EM3D Version 2.0 (preview release 2)

EM3D Version 2.0 (preview release 1)

EM3D Version 1.3

EM3D Version 1.2.5

EM3D Version 1.2.4

EM3D Version 1.2.3

EM3D Version 1.2.2

EM3D Version 1.2

EM3D Version 1.1.3

EM3D Version 1.1.2

EM3D Version 1.1.1

EM3D Version 1.1


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Release Information

EM3D Version 2.0

EM3D 2.0 is now fully implemented in C++/Java. EM3D 2.0's functionality includes loading, aligning, reconstructing projections (including dual tilt datasets), visualizing volume data, segmenting, rendering and calculations. Em3D 2.0 is now multi-threaded and available in 64bit versions for Linux and Windows.

Special Instructions for 64 bit versions

In order to run the Windows x64(64 bit) version of EM3D 2.0, please install the 64 Bit version of the Java SDK and not the Java JRE. The 32 bit and 64 bit versions of EM3D 2.0 can be installed and run at the same time. Simply install the 32 bit version of the Java JRE and the 64 bit version of the Java SDK. As of this release of EM3D 2.0 x64, the 64 bit drivers for various graphics cards do not support a common set of features. To ensure that the 64 bit version of EM3D 2.0 runs on as many different platforms as possible, some advanced rendering features are not available. Primarily this consists of the stereo and the anti-aliasing features. Please use the 32 bit version of EM3D 2.0 for this functionality.

The updated Tutorial is available for release 2.0.

Features release 2.0:

  • Multi-threading, to enhance performance on multi-processor machines
  • Keyboard shortcuts for most functions.
  • Faster calculations in all features
  • More convenient method for setting reconstruction boundries.
  • Reconstruct and segment 2K x 2K datasets
  • Calculations - Uncertainty and Proximity
  • Core Volume - Core out a smaller volume of interest
  • Import Segmentations - Add objects segmented in cored volumes to original volume
  • Unload/Load into RAM - Save memory when working with large datasets
  • Load Single Volumes - Decide whether to load single volumes or not when working with dual tilt datasets
  • Rotation - View rotated volume in Visualization window instantly when changing rotation parameters
  • Rendering - Join objects to groups, visualize surface models using Backface Culling

Known Bugs:

In Windows:

Mac G5s:

Windows 2003 Server x64:

Linux:

When having problems with rendering, try first updating the driver of your graphics card. Please report problems, bugs and crashes to contact@em3d.stanford.edu. Thanks.

New features preview release 2k:

  • Clip Planes - Set arbitrary clipping planes.
  • Cut Planes - Display one or more principal-axis cut planes.
  • Anti Alias - Display the models at 4 levels of alias reduction.
  • Thickness Calculation - Calculates the thickness of an object.

New features preview release 2i:

  • Lighting - Illuminates rendered objects with ambient, positional (point source) and directional (parallel beam) lights with up to 9 light sources.

Please note for preview release 2i: Use "Auto Apply" when changing opacity of rendered objects. Do not select log and cubic at the same time when reconstructing on Mac platforms.

New features preview release 2h:

  • Opacity - Ability to change opacity of rendered objects.
  • Rendering - Rotating, zooming and shifting is faster. Less memory is used to store objects."

New features preview release 2g:

  • Review - Creates animation sequences of projection or volume-slice data.
  • Rendering - Ability to visualize surface models as point, wire or solid models.
  • Lighting - flat and smooth shading both available.
  • Improved segmentation algorithm.

Please note that the Visualization window with enabled objects in combination with the open Render window might not work properly.

New features preview release 2d:

  • Segmentation - The workflow for segmentation has been improved from EM3D 1.X. Segmented objects can now be edited. Also the speed of the segmentation operations have dramatically increased.
  • Basic Rendering - Allows for the visualization of the 3D models.

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EM3D Version 2.0 (preview release 1)

EM3D 2.0 is being implemented in C++/Java. The first preview release is available for downloading.

The functionality is restricted to loading, aligning, reconstructing projections and visualizing volume data. The reconstructed volume can be imported into EM3D V1.2 (IDL version) for segmenting, modeling and analysis.

EM3D V2.0 is available for Windows, Macintosh OS X and Linux i386.

The Tutorial and Manual have been updated appropriately.

New features:

  • Automatic alignment - It is now possible to align projections automatically.
  • Greatly improved speed - Large datasets can be reconstructed at full resolution in a few minutes.
  • Dual axis reconstruction - Takes advantage of the full capability of high end electron microscopes for tomography.

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EM3D Version 1.3 (IDL Version)

New feature - Automatic Region Segmentation (ARS)

This feature allows you to adjust parameters in order to extract objects from regions that have been mapped during segmentation. Please see the User's guide for full description of its use.

Improvements and changes

Maintain objects during core that partially are outside the new volume.

Bug fixes

  • There was a bug that kept isosurfaces from being drawn in the EM3D Visualization window when the High Resolution option was checked.
  • There was an error in the uncertainty calculation that caused a divide by zero error.
  • An error in the uncertainty calculation caused values to be returned 1.5 times larger than they should be.
  • A bug introduced in v1.2.5 caused the Restore function to fail on rotated datasets.

Issues that the User should be aware of

Calculations are not precise and isosurface values are not accurate when the render volume is decimated. If the image volume is decimated values are accurate.

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EM3D Version 1.2.5 (IDL Version)

Changes/Improvements:

The thickness calculation has been modified to the following paradigm:

  • Determine which vertices in the vertex list are truly at the isosurface value, and which are drawn for consistency (due to a bug in the decimated rendering, this is only done when decimation is zero, so for final numbers always use a decimation of zero).
  • Determine the normal vector
  • Determine all vertices that fall within a 15 degree cone along the negative normal from the vertex.
  • Determine the distance between the vertex and all of the vertices found in the cone.
  • The thickness is returned as the average of the distances greater than the mean plus 1 standard deviation of all of the distances.

A new menu option called 'Force Software Rendering' has been added. Select this option when the EM3D Visualization windows or the Render window do not display correctly. This will usually only be necessary on laptops and older computers, that do not have OpenGL graphics cards.

A known bug:

When using a decimated render volume, the CDF for the original volume is used. This means that when doing any calculations for publication please only use undecimated render volumes (the problem only occurs when the volume is decimated in the rendering window, NOT when it is decimated in the EM3D Visualization window).

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EM3D Version 1.2.4 (IDL Version)

In Version 1.2.4 a bug involving the Proximity calculation was addressed.

Instead of fixing the bug, the calculation was re-implemented using 2 methods. The methods are available in the proximity calculation tab as 'Quick' and 'Exhaustive'.

The 'Exhaustive' method finds the true minimum distance of each point in the destination object to the reference object. Although this method is exact it is time consuming for large Reference Objects.

The Quick method is ideal for calculating the proximity of multiple destination objects to the same reference object. The Quick method uses morphological operators to create a 'distance volume' where the value at each point in the volume
is equivalent to its distance from the reference object. Then the proximity for any point in the destination object corresponds to its value in the 'distance volume'. Thus only 1 calculation needs to be done irregardless of the number of destination objects.

Analysis with synthetic and real data indicates that the 'Quick' algorithm yields values 2-9% higher than the values calculated with the 'Exhaustive' search algorithm. So if you do not exact accuracy use the quick calculations, but for publication data, use the exhaustive method.

Recommendations for IDL User's on Windows

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EM3D Version 1.2.3 (IDL Version)

Bugs that have been fixed

  • Rotated objects would shrink every time they were saved.
  • The segmentation area of automatic objects would display improperly when the volume was rotated.
  • Region mapping would fail for objects that bisected the entire volume.

Improvements

  • Rectangular cored volumes can be generated.
  • Objects that were segmented before the volume was cored, are removed if they are not ENTIRELY within the new volume, but remain if they are contained in the new volume.
  • The color scheme for region definition has been changed.

Changes

  • Manual segmentations may now be used to create regions. Previously only automatic regions were used.
  • The Zero button in the EM3D Visualization Window now changes the rotation sliders to the opposite of the current rotations. Previously it set the slider values to zero.

Recommendations for IDL User's on Windows

If you are running out of memory with large datasets, try changing to a 3GB startup by doing the following.

  • right click on My Computer
  • press properties
  • select the advanced tab
  • press Settings in the Startup and Recovery panel
  • press edit in the startup panel
  • add /3GB to the end of the startup line

    example:
    multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Windows XP Professional x64 Edition" /noexecute=optin /fastdetectmulti(0)disk(0)rdisk(0)partition(2)\WINDOWS="Windows XP Professional x64 Edition" /noexecute=optin /fastdetect /3GB
  • save the file
  • restart your computer

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EM3D Version 1.2.2

Bug fixes:

A bug was introduced in V1.2 with the re-segmentation of manual objects when they were rotated. The re-segmentation has been removed, because the error that necessitated it has been fixed.

The position of objects in the rendering window (pos: nm) would be incorrect if either the render volume was decimated and/or the main volume was decimated, this is now fixed, so that coordinates in the render window correspond to coordinates in the main Visualization window.

Improvements:

A minor algorithm change has been made to the renderer, but it reduces the amount of time and memory needed to enable objects. For large datasets, with many small objects this can reduce the time to enable all of the objects by a factor of 50 or more. In addition it allows more objects to be rendered at one time.

Recommendations for IDL User's on Windows:

If you are running out of memory with large datasets, try changing to a 3GB startup by doing the following:

  • right click on My Computer
  • press properties
  • select the advanced tab
  • press Settings in the Startup and Recovery panel
  • press edit in the startup panel
  • add /3GB to the end of the startup line
  • save the file
  • restart computer

Example:

multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Windows XP Professional x64 Edition" /noexecute=optin /fastdetect /3GB

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EM3D Version 1.2

New Features:

In order to facilitate segmentation with high zoom, it is now possible to change the segmentation marker's color, shape, and size.

Changes:

The new thickness calculation generates a more accurate thickness result.

We simplified the user interface for reconstruction.

Bug Fixes:

A bug caused some segmentations to disappear after multiple rotations or saves. This has been fixed.

When manual objects were rotated or restored, they often lost part of their segmented area(red) while keeping their outline(blue or green).

When the volume was rotated, the cross hairs in the transverse views were incorrect. This has been fixed.

Some large temporary files were not being deleted on exit. They are now all deleted when the program exits normally.

For some datasets, TIFF images were being written with their original z-position as the index instead of their slice number. Now the index for the TIFF image matches the slice position in EM3D.

MRC stacks would read in flipped about the X-axis, this has been fixed.

In alignment the fiducial list would grow too long on some platforms making it impossible to access buttons below list. The fiducial list box is now limited to a height of 10 fiducials and becomes scrollable if it exceeds that limit.

Note: If you do encounter anything that you suspect is a bug, please contact us at contact@em3d.stanford.edu and we will gladly address it immediately.

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EM3D Version 1.1.3

New Features:

Quick Start - A quick start button has been added to the File menu. By selecting this button you delay the rendering of the objects until the first time they are enabled. This can greatly speed up loading time, if you are not planning to use the rendering, or only plan to view a small number of objects in a large dataset.

Pre-aligned - We now allow you to load a stack of aligned projections for reconstruction.

Changes:

Alpha Blending - We used to achieve opacity changes through a series of small texture maps. We have replaced this with IDL's alpha blending procedures in order to speed rendering times.

Bug Fixes:

There were several bugs associated with segmentation after the volume had been rotated. The worst of these resulted in data being lost and backup files being over written. Although we believe we have fixed all of these issues, we are a small development team and may have missed something, so if you do encounter anything that you suspect is a bug, please contact us at contact@em3d.stanford.edu and we will gladly address it immediately.

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EM3D Version 1.1.2

New Features:

Import MRC volumes. This allows the importation of volumes that have been reconstructed using other software packages, such as IMOD.

Changes:

The default smoothing for segmentation has been changed from 5 to 10.

Bug Fixes:

  • A bug occurred in some instances where the Stanford License Agreement would appear each time EM3D was started; this has been fixed.
  • Coordinates in the main EM3D window had the origin at the center and in the Rendering window the origin was in the lower left. Now both origins are in the center of the image.
  • When writing 16bit TIFF images from EM3D there was occasionally an issue with signed data, this has been fixed. Note: A new synthetic dataset has been generated using the new version. Please use this in lieu of the previously distributed datasets.
  • If an object was deleted from the render control list of objects, subsequent objects would show the wrong name when double clicked. This has been fixed.

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EM3D Version 1.1.1

Bug Fixes

  • Filenames with multiple periods did not load properly.
  • When reconstructed TIFF files were loaded a variable was not set, so images could not be exported. In order for fix to work images must be loaded from TIFF files again and new state and binary files must be created with V1.1.1 or later.
  • When the render window was open and a new object was segmented, the new object would be unavailable for enabling in the render window until the slider was moved.
  • If Cancel was pressed while renaming a render group the group would be deleted.
  • Occasionally the segmentation control would freeze after the propagate button was pushed.

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EM3D Version 1.1.3

New Features:

Quick Start – A quick start button has been added to the File menu. By selecting this button you delay the rendering of the objects until the first time they are enabled. This can greatly speed up loading time, if you are not planning to use the rendering, or only plan to view a small number of objects in a large dataset.

Pre-aligned – We now allow you to load a stack of aligned projections for reconstruction.

Changes:

Alpha Blending – We used to achieve opacity changes through a series of small texture maps. We have replaced this with IDL’s alpha blending procedures in order to speed rendering times.

Bug Fixes:

There were several bugs associated with segmentation after the volume had been rotated. The worst of these resulted in data being lost and backup files being over written. Although we believe we have fixed all of these issues, we are a small development team and may have missed something, so if you do encounter anything that you suspect is a bug, please contact us at contact@em3d.stanford.edu and we will gladly address it immediately.

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EM3D Version 1.1.2

New Features:

Import MRC volumes. This allows the importation of volumes that have been reconstructed using other software packages, such as IMOD.

Changes:

The default smoothing for segmentation has been changed from 5 to 10.

Bug Fixes:

  • A bug occurred in some instances where the Stanford License Agreement would appear each time EM3D was started; this has been fixed.
  • Coordinates in the main EM3D window had the origin at the center and in the Rendering window the origin was in the lower left. Now both origins are in the center of the image.
  • When writing 16bit TIFF images from EM3D there was occasionally an issue with signed data, this has been fixed. Note: A new synthetic dataset has been generated using the new version. Please use this in lieu of the previously distributed datasets.
  • If an object was deleted from the render control list of objects, subsequent objects would show the wrong name when double clicked. This has been fixed.

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EM3D Version 1.1.1

Bug Fixes

  • Filenames with multiple periods did not load properly.
  • When reconstructed TIFF files were loaded a variable was not set, so images could not be exported. In order for fix to work images must be loaded from TIFF files again and new state and binary files must be created with V1.1.1 or later.
  • When the render window was open and a new object was segmented, the new object would be unavailable for enabling in the render window until the slider was moved.
  • If Cancel was pressed while renaming a render group the group would be deleted.
  • Occasionally the segmentation control would freeze after the propagate button was pushed.

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EM3D Version 1.1

A tutorial and detailed manual were released together with the latest EM3D version 1.1 on October 5, 2004.

On October 6, 2004, a full description of the EM3D approach to model generation together with the results of tests and applications were published in the journal Structure (Ress, D.B., Harlow, M.L., Marshall, R.M. and U.J. McMahan. Methods for generating high-resolution structural models from electron microscope tomography data. Structure : 12 (10):1763-1774, 2005).

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Last modified: 5/1/08

   


This Human Brain Project/Neuroinformatics research is funded by the
National Institute of Mental Health