Neuromantic V1.5.0 Now Available!
Right, it has been a while, but there's an all new singing and dancing version of Neuromantic finally ready. For a full list of what's been changed, see the _README.txt file in the ZIP.
It should be noted that some of the new functions are incomplete and/or not thoroughly tested yet, so may or may not work for you. However, I wanted to get a version out asap after SfN, and the main functionality is all significantly improved. There will be a several more updates in the next few weeks, though, that fix current issues, so keep checking back.
Significant changes include:
* Huge amounts of general updating/bug fixes, including fixing the severe localisation error where SWC files could be generated with either commas or decimal points depending on Windows settings. Neuromantic now loads both regardless and always saves out using the standard decimal point notation (thanks to Padraig Gleeson of UCL for pointing that one out).
* Support for loading MorphML, as well as batch conversion from MorphML to SWC/
* A lot of functionality added to the toolbars, including visualisation options, connectivity editing and segment type options.
* Options to facilitate editing trees, including the ability to reverse sections of dendrites (on toolbar).
* Edit tracking options (added for Duncan Donohue of the Krasnow Institute for editing neurons for NeuroMorpho.org. Enable this in Options->Commenting->Record Changes to keep complete track of any changes made to a reconstruction.
* Additional visualisation modes in 2D with a filled option (like NeuroLucida) and a mode for showing the directionality of the neurites for error-spotting (the arrows point away from the soma).
Some of the functionality is not yet fully completed and thus should be considered as a Beta version.
Statistics calculations
This is the most complete and tested of the new functionality, and may be found on main menu under "statistics". Options exist to calculate a variety of morphometrics, as well as allowing statistical comparison of populations of reconstructions. The results on specific measures may be slightly different from that output by L-Measure due to differing ways in which outlying compartments are excluded from the main calculation.
Graphing options
Allows the plotting of properties such as branch order and euclidean distance, as well as a huge number of other properties. However, it can be a little unreliable at times and needs some more debugging.
3D visualisation
This is certainly the prettiest new addition but, alas, the most unreliable and incomplete for now. There is some (as yet unknown) issue with the OpenGL code, and on some computers it will work perfectly and on others it will freeze and kill the application, and this is independent of the power of the graphics card. Be careful to save any data before trying this, and I'm working hard to find out what on Earth is causing this issue.
Also, at the moment it doesn't downsample the slice images, so don't be surprised if it freezes when you try to display your 3000x3000x100 stack, OK? ;) It was primarily implemented to allow visualisation of MRA data with images resolutions <500 pixels squared or so. When it works, though, it looks beautiful - I'll post some screenshots soon.
Anyway, this mode allows overlaying the current slice data over the reconstruction in the 3D window, as well as masking by luminosity and various levels of translucency. Enable it in the 3D window menu with Overlay->Show Image Stack from the menu.
It should be noted that some of the new functions are incomplete and/or not thoroughly tested yet, so may or may not work for you. However, I wanted to get a version out asap after SfN, and the main functionality is all significantly improved. There will be a several more updates in the next few weeks, though, that fix current issues, so keep checking back.
Significant changes include:
* Huge amounts of general updating/bug fixes, including fixing the severe localisation error where SWC files could be generated with either commas or decimal points depending on Windows settings. Neuromantic now loads both regardless and always saves out using the standard decimal point notation (thanks to Padraig Gleeson of UCL for pointing that one out).
* Support for loading MorphML, as well as batch conversion from MorphML to SWC/
* A lot of functionality added to the toolbars, including visualisation options, connectivity editing and segment type options.
* Options to facilitate editing trees, including the ability to reverse sections of dendrites (on toolbar).
* Edit tracking options (added for Duncan Donohue of the Krasnow Institute for editing neurons for NeuroMorpho.org. Enable this in Options->Commenting->Record Changes to keep complete track of any changes made to a reconstruction.
* Additional visualisation modes in 2D with a filled option (like NeuroLucida) and a mode for showing the directionality of the neurites for error-spotting (the arrows point away from the soma).
BETA FUNCTIONALITY
Some of the functionality is not yet fully completed and thus should be considered as a Beta version.
Statistics calculations
This is the most complete and tested of the new functionality, and may be found on main menu under "statistics". Options exist to calculate a variety of morphometrics, as well as allowing statistical comparison of populations of reconstructions. The results on specific measures may be slightly different from that output by L-Measure due to differing ways in which outlying compartments are excluded from the main calculation.
Graphing options
Allows the plotting of properties such as branch order and euclidean distance, as well as a huge number of other properties. However, it can be a little unreliable at times and needs some more debugging.
3D visualisation
This is certainly the prettiest new addition but, alas, the most unreliable and incomplete for now. There is some (as yet unknown) issue with the OpenGL code, and on some computers it will work perfectly and on others it will freeze and kill the application, and this is independent of the power of the graphics card. Be careful to save any data before trying this, and I'm working hard to find out what on Earth is causing this issue.
Also, at the moment it doesn't downsample the slice images, so don't be surprised if it freezes when you try to display your 3000x3000x100 stack, OK? ;) It was primarily implemented to allow visualisation of MRA data with images resolutions <500 pixels squared or so. When it works, though, it looks beautiful - I'll post some screenshots soon.
Anyway, this mode allows overlaying the current slice data over the reconstruction in the 3D window, as well as masking by luminosity and various levels of translucency. Enable it in the 3D window menu with Overlay->Show Image Stack from the menu.
posted by Neuromantic at
12:25
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