Transient growth f5

[cfrick13]

General overview

• this code performs new analysis with dxdt_48_volume (nuclear transient growth rate) across cell cycle for Figure 5 panel F, and suppFig9 and 10. The analysis is mostly simple and is captured in nuc_morph_analysis/analyses/volume/plot_help.py / plot_dxdt_over_time_by_cell_cycle.py

-this code also introduces a new workflow for identifying short-lived dramatic dips in nuclear volume (suppFigS10).

Volume dip detection and removal (new features and where they come from)

• global_dataset_filtering functions

  add_volume_change_over_25_minute_window --> 'volume_change_over_25_minutes'
  

• filter_out_dips.run_script(df_full) -->

  'volume_dip_peak_mask_at_region', # boolean array, true at all points within peak region(s)
  'volume_dip_peak_mask_at_center', # boolean array, true at all peak centers
  'volume_dip_has_peak', # boolean array, true at all points if there is a peak
  'volume_dip_volume_change_at_center', # magnitude value at each peak center (left_base - peak)
  'volume_dip_volume_change_at_region', # magnitude values at all points within peak region(s) (left_base - peak)
  'volume_dip_width_at_center', # width of the peak at the peak center index
  'volume_dip_width_at_region', # width of the peak at all indices in the peak region
  'volume_dip_max_volume_change', # maximum magnitude value (at all points in array)
  'volume_dip_peak_id_at_center', # peak id at the peak center index
  'volume_dip_peak_id_at_region', # peak id at all indices in the peak region
  'volume_dip_total_number', # total number of peaks
  "volume_dip_removed_um_unfilled", # dips or jumps removed (refilled with nans)
  
  'volume_dips_removed_um_unfilled' # volume trajectories with peak (volume dip) regions removed
  

• then compute growth rate to get -->

  `dxdt_48_volume_dips_removed_um_unfilled`
  

• and compute neighbors to get -->

  'neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_90um'
  'neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_whole_colony'
  

New/updated figures generated in this code

Figure 5 panel F, G, H

* _note: only change to H was N value correction_

SuppFig S9 F,G,H

* _note: only change to F was x-axis values corrected to be in µm/hr_ * _note: only change to H was N value

SuppFig S10 (all)

[jcass11]

Suggested change

	load_local=True,
	load_local=False,

[cfrick13]

updates

I made a few more edits to add clarity and then merged the dev branch.

tests

Reran write_data_for_colorizer.py successfully.
Rerunning run_all_manuscript_worfklows.py.

[jcass11]

Took a look through all the files and it looks great! Did not re-test since it sounds like you're on top of that

[cfrick13]

update:
====== Successes ======
figure_1_dataset (393.7s) (50.8GB)
figure_3_s4_height_density (317.3s) (44.6GB)
figure_4_s8_volume_trajectories (67.1s) (27.1GB)
figure_6_s11_compensation (77.9s) (27.1GB)
figure_7_s13_s14_lineage (259.2s) (27.1GB)
figure_s12_feeding_control (86.2s) (20.3GB)
figure_s15_linear_regression_model (1460.5s) (27.1GB)
figure_s19_transition_point (15.4s) (27.2GB)
figure_s1_cell_health (13.5s) (23.7GB)
figure_s20_precision_error (7.2s) (5.3GB)
figure_s2_s3_s18_segmentation_model_validation (155.9s) (8.4GB)
figure_s7_growth_outliers (78.3s) (27.9GB)
====== Failures ======
figure_5_s9_s10_local_growth (154.7s) (43.9GB). TypeError expected string or bytes-like object. See stack trace above.
figure_s6_s16_inhibitors (29.6s) (13.4GB). AssertionError . See stack trace above.
====== 12 succeeded 2 failed ======

[cfrick13]

====== figure_5_s9_s10_local_growth ======
Traceback (most recent call last):
File "/allen/aics/assay-dev/users/Frick/PythonProjects/repos/nucmorph_dev/nuc-morph-analysis/nuc_morph_analysis/utilities/workflow_runner.py", line 38, in _runjob
job()
File "/allen/aics/assay-dev/users/Frick/PythonProjects/repos/nucmorph_dev/nuc-morph-analysis/run_all_manuscript_workflows.py", line 43, in figure_5_s9_s10_local_growth
import nuc_morph_analysis.analyses.volume.FigS10_workflow
File "/allen/aics/assay-dev/users/Frick/PythonProjects/repos/nucmorph_dev/nuc-morph-analysis/nuc_morph_analysis/analyses/volume/FigS10_workflow.py", line 123, in
axlist = type_axlist(axlist_untyped)
File "/allen/aics/assay-dev/users/Frick/PythonProjects/repos/nucmorph_dev/nuc-morph-analysis/nuc_morph_analysis/lib/visualization/matplotlib_to_axlist.py", line 21, in type_axlist
plt_axis_list = cast(List[Axes], cast(NDArray, plt_axis_np).tolist())
AttributeError: 'list' object has no attribute 'tolist'
====== Failures ======
figure_5_s9_s10_local_growth (161.4s) (39.6GB). AttributeError 'list' object has no attribute 'tolist'. See stack trace above.
====== 1 failed ======

[cfrick13]

Got it working! Will merge now!
====== Successes ======
figure_5_s9_s10_local_growth (236.4s) (41.3GB)
====== 1 succeeded ======