users
users > RE: Current CMTK instructions for non-coders?
Apr 27, 2022 10:04 AM | Sandor Kovacs
RE: Current CMTK instructions for non-coders?
Hi, Lets just try to run CMTK and the
Fiji GUI on your setup first, Probably I should add this to the
readme but your problem could be that there is a space or a special
character in any of the file paths, if not can you tell me
which operating system you want to use ?
I think Torsten's guide is very useful when you use it while exploring CMTK in the command line, for example running the "cmtk --help" command, you can add the help options to any command to see what kind of operations and parameters you can use and what is the basic syntax, you can even find some basic explanations there. I encourage you to actually try the examples in the userguide, while reading the help pages, and experimenting with the options. CMTK real challange that it requires some understanding of the underlying image mathematics for effective use, coding is really just typing in the commands following the syntax on the help pages, maybe add some basic logic combining it with bash commands.
Originally posted by c_mckellar:
I think Torsten's guide is very useful when you use it while exploring CMTK in the command line, for example running the "cmtk --help" command, you can add the help options to any command to see what kind of operations and parameters you can use and what is the basic syntax, you can even find some basic explanations there. I encourage you to actually try the examples in the userguide, while reading the help pages, and experimenting with the options. CMTK real challange that it requires some understanding of the underlying image mathematics for effective use, coding is really just typing in the commands following the syntax on the help pages, maybe add some basic logic combining it with bash commands.
Originally posted by c_mckellar:
Thanks, I did glance through that User Guide but
I don't think there are any sections in it that would help a
non-coder. Here's how explicit I'm trying to make the instructions
to align fly brains, below. I haven't been able to find any
instructions for the CMTK interface in Fiji, since the link to the
flybrain wiki is down. Haven't been able to get CMTK to work from
Fiji, myself. Using the "Registration Parameter Preset" of the full
brain and changing no other settings, the Log just says
"Registration warp failed, Registration affine failed." So I
currently only wrote pre-prep instructions:
Here's the type of thing I'm trying to write:
Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Update, then reboot your computer.
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration...
Here's the type of thing I'm trying to write:
Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Update, then reboot your computer.
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration...
Threaded View
| Title | Author | Date |
|---|---|---|
| c_mckellar | Apr 14, 2022 | |
| Torsten Rohlfing | Apr 15, 2022 | |
| c_mckellar | Apr 19, 2022 | |
| Sandor Kovacs | Apr 27, 2022 | |
| c_mckellar | May 5, 2022 | |
| Sandor Kovacs | May 5, 2022 | |
| c_mckellar | May 7, 2022 | |
| Sandor Kovacs | May 9, 2022 | |
| c_mckellar | May 9, 2022 | |
| Greg Jefferis | Apr 14, 2022 | |