A description of the project: I'm trying to reconstruct certain parts of the brain (subthalamic nucleus, red nucleus, etc.) by cutting human brain blocks and...
I think I know how to fix this now after reading the FAQ. How do I change the area of a trace, namely from negative to positive? ... taking ... section...
Hello, I have been working with dendritic spines 3D reconstructions and I would like to experiment with "morphological averaging". Considering each spine as a...
Dear John, What happened to synapse website, http://www.synapses.mcg.edu/ ? I can not access it for a while. It is one of my favorites. Jianli fiala_jc...
Dear John, I'm wondering how one could extract from the Tranfrom element in the section data files the exact tranformation of the contours and/or images. The...
Elaine, The transformation equations are given in the Fiala & Harris, 2001, paper: http://synapses.bu.edu/tools/sightings/jamia.pdf Let me know if you need...
Apologies for not searching the archives first.... I am on the point of leaving for a weeks' holiday, but my boss wants me to ask this question before I go...
Cornelia, It depends on your traces, especially how many trace segments you create. You need enough segments so that some segments are close to one branch...
I am doing point alignment of 800 images from light microscopy as I have no fiducial markers in my specimen. The first 50 images can be very well aligned, but...
mfriis2204, Try to follow the alignment tips given in: http://synapses.bu.edu/tools/chapter10.pdf Since you can detect the rotational offset it is also...
Robert, Surface area is the length of each trace times the section thickness summed over all traces of the object, while flat area treats open and closed...
Hi, John. When I click _Object_ and then _List objects_, reconstruct just stays at 'Reading.' When I quit Reconstruct, and then re-install it from the Yahoo...
It's probably not you, it's probably your computer. I've noticed that every once in a while this happens on my computer, unexpectedly the Object List reading...
Dear All Hi , I am looking for a suitable pen mouse to use that in the reconstruct software, i would like to sketch and drowing tracees directly on screen, I...
Hi Reza, I've been using Reconstruct for several years now with a Wacom Cintiq digitizing pad. The Cintiq has an embedded flat panel screen so you can draw...
Hello all quick question, I have just aligned a series of EM images (65 images in stack, ~ 100Mb, each). I am trying to export the output files from ...
BobbyK, You can search the Messages on the Users Group for an answer to this question: http://tech.groups.yahoo.com/group/reconstruct_users/message/58 Or you...
Is there a way to make the 3D images (e.g. a reconstructed dendrite) look 'smoother' without having to output to a different program? Reconstruct and Photoshop...
Yes. The biggest issue for smoothing is how good the alignment is. But when there are a few misalignments these can sometimes be eliminated by adjusting the...
Brian, If you mean the centroids of the traces for an object: Turn on the centroids and z-position output in the Trace List from the Series Options, and then...
I also have this problem with my computer as well. I tried to quit all the programs but it still didn't work. Normally I restart Windows and reopen the ...
Hi John First of all, thank you for making this great software available for the people involve in 3D reconstructions. Well John, I have a few problems with...
Hi John First of all, thank you for making this great software available for the people involve in 3D reconstructions. Well John, I have a few problems with...
Demian, The wildfire region growing is based on the pixel intensities displayed on the screen and can make very complex traces with many segments that carry...
Dear John Thank you for your comments, I'll take a look at that. The merge works fine, the only problem is when using wildfire several times then the program...
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