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Add new set of features for morphometrics #84

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Add new set of features for morphometrics #84

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db9adc4
Add new morphometrics configurations to test
EmilieDel Nov 17, 2022
6440508
Add parameters for extract-features-morphometrics
EmilieDel Nov 17, 2022
037297d
Fix indentation petilla morphometrics
EmilieDel Nov 17, 2022
a7e5262
Add train step
EmilieDel Nov 18, 2022
7212ff0
Add evaluation step
EmilieDel Nov 18, 2022
49693a2
Add update of morphometrics dvc repro
EmilieDel Nov 18, 2022
ff94bad
Add new updates from morphometrics experiment
EmilieDel Nov 21, 2022
6d0b6fd
Try petilla without problematic parameter
EmilieDel Nov 21, 2022
01a7115
Add the configuration files
EmilieDel Nov 21, 2022
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2,485 changes: 1,703 additions & 782 deletions dvc/dvc.lock
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14 changes: 14 additions & 0 deletions dvc/dvc.yaml
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Expand Up @@ -2691,6 +2691,20 @@ stages:
- training/checkpoints-morphometrics/${key}
desc: "Train M-type classifier with morphometric input features (tabular data)"

evaluate-morphometrics:
foreach: ${evaluate-morphometrics}
do:
cmd: >-
morphoclass -vv evaluate performance
training/checkpoints-morphometrics/${item}/checkpoint.chk
evaluation/${item}.html
deps:
- training/checkpoints-morphometrics/${item}/checkpoint.chk
outs:
- evaluation/${item}.html
- evaluation/${item}
desc: "Evaluate M-type classifier with morphometric input features (tabular data)"

transfer-learning:
foreach: ${transfer_learning.models}
do:
Expand Down
26 changes: 26 additions & 0 deletions dvc/extract-features-morphometrics/configs/morphometrics_config_allen.yaml
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@@ -0,0 +1,26 @@
morphology:
total_length_per_neurite:
- mean
total_area_per_neurite:
- mean
total_volume_per_neurite:
- mean
total_depth:
- mean
total_height:
- mean
total_width:
- mean
neurite:
number_of_sections:
- sum
section_bif_lengths:
- mean
- std
section_path_distances:
- max
section_radial_distances:
- max
neurite_type:
- BASAL_DENDRITE
- APICAL_DENDRITE
48 changes: 48 additions & 0 deletions dvc/extract-features-morphometrics/configs/morphometrics_config_lauturns.yaml
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morphology:
total_length_per_neurite:
- sum
total_area_per_neurite:
- sum
total_volume_per_neurite:
- sum
number_of_neurites:
- sum
total_depth:
- mean
total_height:
- mean
total_width:
- mean
neurite:
number_of_bifurcations:
- sum
number_of_leaves:
- sum
total_length_per_neurite:
- max
section_branch_orders:
- max
section_bif_lengths:
- median
section_term_lengths:
- median
section_tortuosity:
- median
- max
local_bifurcation_angles:
- mean
- min
- max
partition_asymmetry:
- mean
total_area_per_neurite:
- mean
segment_meander_angles:
- mean
- max
section_radial_distances:
- max
neurite_type:
- AXON
- BASAL_DENDRITE
- APICAL_DENDRITE
22 changes: 22 additions & 0 deletions dvc/extract-features-morphometrics/configs/morphometrics_config_petilla.yaml
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neurite:
number_of_sections:
- mean
local_bifurcation_angles:
- mean
partition_asymmetry:
- mean
section_tortuosity:
- mean
diameter_power_relations:
- mean
sholl_frequency:
- mean
- max
segment_radii:
- mean
segment_taper_rates:
- mean
neurite_type:
- AXON
- BASAL_DENDRITE
- APICAL_DENDRITE
20 changes: 20 additions & 0 deletions ...xtract-features-morphometrics/configs/morphometrics_config_petilla_without_parameter.yaml
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neurite:
number_of_sections:
- mean
local_bifurcation_angles:
- mean
partition_asymmetry:
- mean
section_tortuosity:
- mean
sholl_frequency:
- mean
- max
segment_radii:
- mean
segment_taper_rates:
- mean
neurite_type:
- AXON
- BASAL_DENDRITE
- APICAL_DENDRITE
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-L1/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-L23/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-L4/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-L5/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-L6/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-merged-bc-merged/.gitignore
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/all
/allen
/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/in-merged/.gitignore
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/all
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/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/janelia-L5/.gitignore
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/all
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/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/pc-L2/.gitignore
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/all
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/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/pc-L3/.gitignore
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/all
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/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/pc-L4/.gitignore
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/all
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/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/pc-L5/.gitignore
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/all
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/lauturns
/petilla
3 changes: 3 additions & 0 deletions dvc/extract-features-morphometrics/pc-L6/.gitignore
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/all
/allen
/lauturns
/petilla
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