For reconstructions from 3D image stacks, we have been quite satisfied with the Neuromantic freeware:

https://www.reading.ac.uk/neuromantic/body_index.php

It does what it is supposed to, with no bells and whistle that complicate matters more than they help. With Neuromantic, I have put dozens of undergraduate students on the manual reconstruction work, they get their lab experience, we get our reconstructions, everybody's happy. We've done >150 reconstructions in the lab this way. Works great, but support is nil and updates rare.

I have heard good things about Fiji/Simple Neurite Tracer but never tried it. There is also Herman Cuntz's TREES toolbox (http://www.treestoolbox.org), which is more advanced. Finally, you might benefit from the option not to reconstruct at all (Ferreira et al: Neuronal morphometry directly from bitmap images. Nature Methods 2014 DOI:10.1038/nmeth.3125.).

All of this requires 3D image stacks though, so you do not work "live" like people often do with Neurolucida. However, working offline comes with advantages too.

For our work with Neuromantic, see below, in particular Blackman et al:

Blackman AV, Grabuschnig S, Legenstein R, & Sjöström PJ: A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling. Frontiers in Neuroanatomy (2014) 8:65, DOI: 10.3389/fnana.2014.00065.

Lalanne T, Abrahamsson T, & Sjöström PJ: Using Multiple Whole-Cell Recordings to Study Spike-Timing-Dependent Plasticity in Acute Neocortical Slices. Cold Spring Harb Protoc (2016) 10.1101/pdb.prot091306

Buchanan KA, Blackman AV, Moreau AW, Elgar D, Costa RP, Lalanne T, Tudor Jones AA, Oyrer J, & Sjöström PJ: Target-Specific Expression of Presynaptic NMDA Receptors in Neocortical Microcircuits. Neuron (2012) 75:451-466.

Lalanne T, Oyrer J, Mancino A, Gregor E, Chung A, Huynh L, Burwell S, Maheux J, Farrant M, and Sjöström PJ: Synapse-specific expression of calcium-permeable AMPA receptors in neocortical layer 5. The Journal of Physiology (2016) 594(4):837-861.

Or imaris....but it’s more expensive

Hi,

You can either use Fiji Image J plugins as suggested before or Neuromantic which is free of charge and quite similar to Neurolucida (you have to acquire pictures first and reconstruct, even 3D, later though)

Hope it helps

Hello,

Definitely, I would go for Fiji image J with the neurite tracer + the geodesis plugins https://imagej.net/Simple_Neurite_Tracer. It is free and easier than neurolucida

Have a good day

Fabien

For reconstructions from 3D image stacks, we have been quite satisfied with the Neuromantic freeware:

https://www.reading.ac.uk/neuromantic/body_index.php

It does what it is supposed to, with no bells and whistle that complicate matters more than they help. With Neuromantic, I have put dozens of undergraduate students on the manual reconstruction work, they get their lab experience, we get our reconstructions, everybody's happy. We've done >150 reconstructions in the lab this way. Works great, but support is nil and updates rare.

I have heard good things about Fiji/Simple Neurite Tracer but never tried it. There is also Herman Cuntz's TREES toolbox (http://www.treestoolbox.org), which is more advanced. Finally, you might benefit from the option not to reconstruct at all (Ferreira et al: Neuronal morphometry directly from bitmap images. Nature Methods 2014 DOI:10.1038/nmeth.3125.).

All of this requires 3D image stacks though, so you do not work "live" like people often do with Neurolucida. However, working offline comes with advantages too.

For our work with Neuromantic, see below, in particular Blackman et al:

Blackman AV, Grabuschnig S, Legenstein R, & Sjöström PJ: A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling. Frontiers in Neuroanatomy (2014) 8:65, DOI: 10.3389/fnana.2014.00065.

Lalanne T, Abrahamsson T, & Sjöström PJ: Using Multiple Whole-Cell Recordings to Study Spike-Timing-Dependent Plasticity in Acute Neocortical Slices. Cold Spring Harb Protoc (2016) 10.1101/pdb.prot091306

Buchanan KA, Blackman AV, Moreau AW, Elgar D, Costa RP, Lalanne T, Tudor Jones AA, Oyrer J, & Sjöström PJ: Target-Specific Expression of Presynaptic NMDA Receptors in Neocortical Microcircuits. Neuron (2012) 75:451-466.

Lalanne T, Oyrer J, Mancino A, Gregor E, Chung A, Huynh L, Burwell S, Maheux J, Farrant M, and Sjöström PJ: Synapse-specific expression of calcium-permeable AMPA receptors in neocortical layer 5. The Journal of Physiology (2016) 594(4):837-861.

Dear Per Jesper Sjöström,

Is Neuromantic software also suited for 3D dendritic spine count and classification?

Thank you in advance,

Best,

Hi Joseph,

If you are fed up with spending weeks for manually tracing just a handful of neurons, you might want to take a look at our brand new online neuron tracing service: https://ariadne.ai/lmtrace/

Just upload your images and we take it from there. Made by neuroscientists for neuroscientists.

Use the coupon LMtraceKICKOFF to unlock your personal 15% discount.

Best,

Adrian

Hello Per Jesper Sjöström (and anyone willing to help),

I'm currently trying to use Neuromantic for reconstructing dendrites stained using the Golgi-Cox method. The online demo videos for the software look great and I would love to use this tool for my own analysis, but I am having issue uploading .Tif files into the program. I'm currently trying to use Neuromantic V1.6.3 and according to the online forum (scantly visited/updated these days), V1.7.5 was created circa 2010, but the link provided for the download no longer connects, and I was wondering if you have access to this version or if you have any suggestions as to how to upload images in V1.6.3. Thank you so much for your time--I truly appreciate any help.

Hi Nicholas,

You might want to take a look at our online neuron tracing service: https://ariadne.ai/lmtrace/

Depending on the cell and dataset type we could also make you a custom offer. In addition, I can highly recommend our open-source tool https://knossos.app/ for manual skeleton tracing of neurites in light microscopy datasets. It's very intuitive and efficient and has been test extensively. Plus, it comes with a Python interface that allows you to write your own plugins. Our developers are very responsive in case you run into problems, just post an issue on github (https://github.com/knossos-project/knossos)

You could try this webKnossos:

https://www.nature.com/articles/nmeth.4331

https://scalableminds.com/webknossos

Nicholas Deems have you managed to solve your problems, i.e. have you been able to use Neuromantic? If not, perhaps if you specify the nature of the problems you encountered, someone can help. Have you tried opening some small test .tif files? It's been a while since I've used the software, but I was always a big fan of Neuromantic. The developer's email address is listed in the google groups forum where you found the v1.7.5 link, by the way.

The source tree contains a folder with some "test stacks" from the developer:

https://sourceforge.net/p/neuromantic/code-0/2/tree/trunk/Test%20Stacks/

The trunk folder contains a compiled .exe, but I believe it may require additional libraries, and I don't have the wherewithal to tell you what's needed to get this working. Darren Myatt, the developer, explains a bit what's needed if you wish to compile it yourself: https://groups.google.com/forum/#!topic/neuromanticusergroup/PbzzZ49bHrM