Bacteria Density Analyzer
Contents:
Introduction to “Bacteria Density Analyzer”
Bacteria Density Analyzer: Abstract
Bacteria Density Analyzer: User’s guide
Bacteria Density Analyzer
bacteria_density.bd_worker module
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bacteria_density.bd_worker module
class
bacteria_density.bd_worker.
BacteriaDensityWorker
[source]
Bases:
object
add_measurement_channel
(
name
,
ch
)
[source]
add_region
(
id_str
,
coordinates
)
[source]
are_measures_generated
(
)
[source]
are_medial_paths_generated
(
)
[source]
are_regions_exported
(
)
[source]
are_skeletons_generated
(
)
[source]
chunks_as_json
(
)
[source]
chunks_from_json
(
as_json
)
[source]
error
(
msg
)
[source]
export_processed_set
(
)
[source]
export_regions
(
)
[source]
get_measurement_channels
(
)
[source]
get_processed_metrics
(
)
[source]
get_rank
(
id_str
,
bbox
)
[source]
get_segmentation_channel
(
)
[source]
info
(
msg
)
[source]
make_mask_and_skeleton
(
)
[source]
make_measures
(
)
[source]
make_medial_path
(
)
[source]
make_plots
(
)
[source]
merge_measures
(
)
[source]
recover
(
)
[source]
recover_calibration
(
)
[source]
recover_images
(
)
[source]
recover_metrics
(
)
[source]
recover_regions
(
)
[source]
save_measurement_channels
(
)
[source]
save_metrics
(
)
[source]
save_original
(
name
,
image
)
[source]
save_regions
(
)
[source]
save_segmentation_ch
(
)
[source]
set_binning_distance
(
dist
)
[source]
set_calibration
(
calibration
,
unit
=
'µm'
)
[source]
set_merge_measures
(
merge
)
[source]
set_segmentation_channel
(
ch
,
name
=
'Nuclei'
)
[source]
set_starting_hint
(
id_str
,
start
)
[source]
set_threshold_factor
(
factor
)
[source]
set_working_dir
(
working_dir
)
[source]
state_as_json
(
)
[source]
use_metric
(
name
,
to_use
)
[source]
warning
(
msg
)
[source]
bacteria_density.bd_worker.
launch_analysis_workflow
(
)
[source]
bacteria_density.bd_worker.
launch_recover_workflow
(
)
[source]
bacteria_density.bd_worker.
launch_synthetic_workflow
(
)
[source]