Hi, I was recently introduced to this really great program, and was attempting to use it to do some traces from muticolor (3 channels) confocal stacks using...
Hello, I'm a new user with this great program, and recently ran into a problem. In dealing with the thickness of my TEM sections, I noticed some parts are...
Jean, Thanks for pointing out the limitation on the Hue parameter. I'll look into implementing a solution. Originally, I used RGB parameters but it was very...
Shannon, No. When using serial sections you should rely on the fact that any thinning in one part of one section will be offset by a corresponding (after...
Also Shannon, how are you estimating section thickness? Are you using the cylindrical diameters method? If not, you may want to read the following paper - pdf...
Hi John, (Sorry if you receive this message a second time) Thanks a lot for your quick answer and the very helpful piece of advice concerning shortcut usage. I...
Jean, Try version 1.0.7.7 just posted at: http://groups.yahoo.com/group/reconstruct_users/files/ I think this fixes the hue wrap around issue. Also it include...
Hi John, Awesome! Thanks for taking care of the hue issue so fast! It works perfectly now. I will now ask Ju how to stop the wildfire before it reaches the end...
Hi John This a very basic problem and probably down to my ineptitude but I am having problems when exporting a single montaged section. I have tried exporting...
Steve, The image is not zipped. Try opening the new series created by the export operation. You can then see the image and locate the file name from the domain...
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 ...
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