synapseweb / reconstruct

Source code for Reconstruct

Reconstruct

Here at GitHub is the original Source code for Reconstruct - which was last compiled in 2007 and the Executible is available at: https://sites.cns.utexas.edu/synapseweb/software-0

Software

Reconstruct Downloads for Windows and other Platforms

• Reconstruct 1.1.0.0 (32-bit Windows)

• Reconstruct 1.1.0.1 (64-bit Windows)

• Development Version (64-bit Windows) (SHA1 sum)

• Java Version (All Platforms)

with Help Manual and example.ser (7.38MB) [Version 1.1.0.0 August 20, 2007]

System Requirements:

• Microsoft Windows (XP/Vista/7/8)
• Pentium processor
• 10 Mb of disk space for program files
• at least 128 Mb of RAM

Further reading:

• Quick Start -- to get started using the software (User Manual Ch 1).
• Intro for Beginners and Reconstruct Basics -- quick intros to the basic elements of Reconstruct.
• User Manual -- revised by Dr. Karin Sorra and Dr. Kristen Harris (2009).
• Fiala JC (2005) Reconstruct: A free editor for serial section microscopy. J Microscopy.
• Fiala JC, Harris KM (2001) Cylindrical diameters method for calibrating section thickness in serial electron microscopy. J Microscopy.
• Harris KM, Spacek J, Bell ME, Parker PH, Lindsey LF, Baden AD, Vogelstein JT, Burns R (2015) A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development. Sci Data Sep 1;2:150046. PMCID: PMC4555877. (PDF; Tables)

Reconstruct was written by John C. Fiala, Ph.D.

For more info go to Reconstruct History and Citations. For help with specific questions, contact the Reconstruct Yahoo User's Group.

Reconstruct was created with funding, in part, from the National Institutes of Health and the Human Brain Project under grants (P30 HD18655, R01 MH/DA 57351, and R01 EB 002170).

Permission to use, copy, and redistribute Reconstruct is granted without fee under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.

(This software is distributed in the hope that it will be useful, but without any warranty, including the implied warranty of merchantibility or fitness for any particular purpose. For details read the terms of the GNU General Public License when installing the software.)

• Java Version

• CodeBlocks C++ Experiments

• Blender Experiments

• GitHub Notes

reconstruct's Issues

How to output a binary mask (binary volume) for each object?

After finishing the tracing and the object is shown in the object list. I wish to output the binary volume of the whole object. How can I achieve that?

How to map between microns and pixels?

Hi, I am trying to extract patches from the original image based on the drawn contours by applying the inverse transform to the contour and placing it over the original image. However, we cannot find the ratio conversion between microns and pixels in the xml file.

How do we find the ratio between microns and pixels in the xml file? I can't seem to find the answer in the source code. Thank you!

• Angela

Properly Handle JPEG Images

Version 1.2.0.1
Doesn't open JPEG Images - Program crashes
This was working in 1.1.0.x
@k34harris @tmbartol

How to find contour offset?

Hi, I am trying to extract information using the xml file to compute the inverse transform of a contour and overlay it with the original image in a a section. I am not trying to use the GUI for RECONSTRUCT, as I would like to do this automatically in python.

My problem is that the x and y coordinates in the image space of a section do not match with the x and y coordinates in the contour space in the same section. I've included example images to try to illustrate the problem.

You can see that in the first image, the coordinates are in pixels and they are of a different number than in the second image, where the coordinates are in microns. I am talking about the 'position' as seen in the bottom bar. The mouse is in the same position for both images.

Where in the data (xml, code, ??) can I find the translation and mapping between these two coordinate systems? Thank you.

Integrated Help Missing

Version 1.2.0.1

Integrated help commands do not work:

Message: Cannot open the file: manual.chm.
Message: Cannot open the file: keycmds.chm.
Message: Cannot open the file: mousecmds.chm.