GitHub - miroslavradojevic/bigneuron: Automated neuron reconstruction algorithms - entries for the BigNeuron project. It's a set of methods - implemented as plugins for vaa3d platform - that were gradually developed for the project. Repository keeps different versions in each directory

miroslavradojevic / bigneuron Public

Notifications You must be signed in to change notification settings
Fork 0
Star 1

Automated neuron reconstruction algorithms - entries for the BigNeuron project. It's a set of methods - implemented as plugins for vaa3d platform - that were gradually developed for the project. Repository keeps different versions in each directory

View license

1 star 0 forks Branches Tags Activity

Star

Notifications

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
Advantra		Advantra
Advantra_bigneuronsubmission		Advantra_bigneuronsubmission
NeurAuto		NeurAuto
NeuronChaser		NeuronChaser
NeuronChaserX		NeuronChaserX
NeuronFloater		NeuronFloater
newwork		newwork
.hgignore		.hgignore
ImportTextImageSequence.ijm		ImportTextImageSequence.ijm
LICENCE		LICENCE
README		README
expelled.txt		expelled.txt
expelled.zip		expelled.zip
hgpush.sh		hgpush.sh

Repository files navigation

Parameter configurations, basic info, terminal calls with parameter configurations.


############################################
####            Neuronchaser            ####
############################################
vaa3d -x NeuronChaser -f help
############################################
**** Usage of NeuronChaser tracing **** 
vaa3d -x NeuronChaser -f nc_func -i <inimg_file> -p <channel> <scal perc znccTh Ndir angSig Ni Ns zDist saveMidres>
inimg_file          The input image\n");
channel             Data channel for tracing. Start from 1 (default 1).
scal                Scale (5, 20] pix.
perc                Percentile [50, 100].
znccTh              Correlation threshold [0.5, 1.0).
Ndir                nr. directions [5, 20].
angSig              Angular sigma [1,90] degs.
Ni                  nr. iterations [2, 50].
Ns                  nr. states [1, 20].
zDist               z layer dist [1, 4] pix.
saveMidres          Save midresults 0-no, 1 -yes.
outswc_file         Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 90 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 95 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 99 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 90 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 95 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 99 0.6 15 60 30 5 1 0


############################################
####   Advantra (bigneuron submission)  ####
############################################
vaa3d -x Advantra -f help
############################################
**** Usage of Advantra tracing **** 
vaa3d -x Advantra -f advantra_func -i <inimg_file> -p <scal bratio perc znccTh Ndir angSig Ni Ns zDist>
inimg_file          The input image
scal                Scale (5, 20] pix.
bratio              Background ratio (0, 1].
perc                Percentile [50, 100].
znccTh              Correlation threshold [0.5, 1.0).
Ndir                nr. directions [5, 20].
angSig              Angular sigma [20,90] degs.
Ni                  nr. iterations [2, 50].
Ns                  nr. states [1, 20].
zDist               z layer dist [1, 4] pix.
outswc_file         Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.3 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.3 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.8 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.8 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.3 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.3 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.8 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.8 99 0.6 15 60 30 5 1


############################################
####           NeuronChaserX            ####
############################################
vaa3d -x NeuronChaserX -f help
############################################
**** Usage of NeuronChaserX **** 
vaa3d -x NeuronChaserX -f ncx_func -i <inimg_file> -p <scal bratio perc znccTh Ndir angSig Ni Ns zDist>
inimg_file          The input image
scal                Scale (5, 20] pix.
bratio              Background ratio (0, 1].
perc                Percentile [50, 100].
znccTh              Correlation threshold [0.5, 1.0).
Ndir                nr. directions [5, 20].
angSig              Angular sigma [20,90] degs.
Ni                  nr. iterations [2, 50].
Ns                  nr. states [1, 20].
zDist               z layer dist [1, 4] pix.
outswc_file         Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.3 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.3 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.8 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.8 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.3 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.3 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.8 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.8 99 0.6 15 60 30 5 1

############################################
############################################
############################################

On local machine Advantra plugin was replaced with the new Advantra, complete redesign of the bigneuron submission plugin. New code is placed in Advantra directory while the one submitted to the bigneuron was stored in Advantra_bigneuron 

############################################
####              Advantra              ####
############################################
vaa3d -x Advantra -f help
############################################
---- ADVANTRA usage ----
vaa3d -x Advantra -f advantra_func -i <inimg_file> -p <sigmax msiter sig2radius znccth kappa step ni np zdist>
inimg_file          The input image.
sigmax              Max Gaussian cross-section sigma.
msiter              # refinement iterations.
seedscmin           minimum seed score (uint8 greylevels 0-255).
znccth              Correlation threshold.
kappa               Von Mises variance.
step                Prediction step.
ni                  # trace iterations.
np                  # trace particles.
zdist               z layer dist.
blurring            blurring (0-no,1-yes).
grouping            grouping method (0-cylinder,1-sphere).
nodepp              nodes per pixel trace density limit.
outswc_file         Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
~/vaa3d/vaa3d_tools/bin/vaa3d64.app/Contents/MacOS/vaa3d64 -x Advantra -f advantra_func -i image.v3dpbd -p 3 2 0.001 0.4 3 2 20 25 2 0 1 9