Started at: {{starttime}}
Finished at: {{endtime}}

Parameters

General

Data folder: {{basedir}}
Output folder: {{outdir}}
Log path: {{logpath}}
Regular expression: {{reg}}
Extension: {{ext}}
Cores: {{ncores}}
Skipped steps: {% if skip|type == []|type or skip|type == ()|type %}
    {% for ss in skip %}
  • {{ss}}
    • {% endfor %}
{% else %} {{skip}} {% endif %}
Verbose: {{verbose}}
Debug mode: {{debugging}}
Output suffix: {{suffix}}

Images

Pixel aspect: {{aspect}}
DNA channel names: {% if dna_names|type == []|type or dna_names|type == ()|type %}
    {% for dn in dna_names %}
  • {{dn}}
    • {% endfor %}
{% else %} {{dna_names}} {% endif %}
Signal channel names: {% if sig_names|type == []|type or sig_names|type == ()|type %} {{ sig_names|join(', ') }} {% else %} {{sig_names}} {% endif %}

Plot

Plotting: {{plotting}}
Font-size {{fontsize}}
Number of bins {{nbins}}
Sigma (for smoothing): {{sigma_smooth}}
Sigma (for density): {{sigma_density}}

Segmentation

{% if seg_type == '3D' %} {% endif %}
Segmentation type {{seg_type}}
Radius interval: {{radius_interval}}
Adaptive threshold box side: {{adp_thr}}
Remove Z-stack object tips (top/bottom): {{rm_z_tips}}
Offset: {{offset}}
Minimum Z size {{min_z_size}}

Analysis

Analysis type {{an_type}}{% if 'Mid-section' == an_type %} ({{mid_type}}){% endif %}
Nuclear selection features: {% if nsf|type == []|type or nsf|type == ()|type %}
    {% for nf in nsf %}
  • {{nf}}
    • {% endfor %}
{% else %} {{nsf}} {% endif %}
Partial nucleus erosion (3D): {{part_n_erosion}}
Distance type {{dist_mode}}
Normalize distance: {{norm_d}}
Rescale deconvolved images: {{rescale_deconvolved}}

Notes

{{notes}}

Dataset description

Found {{conds|length}} conditions.

{% for i in range(conds|length) %} {% endfor %}

Boxplots

{% for i in range(conds|length) %} {% endfor %} Size per nucleus boxplot not found Shape per nucleus boxplot not found mean(DNA) per nucleus boxplot not found sum(DNA) per nucleus boxplot not found DNA per pixel boxplot not found Signal per pixel boxplot not found

Segmentation and nuclear selection

Results

Number of pixels

{% for i in range(conds|length) %} Number of pixels not found {% if an_type == '3D' %} Number of pixels not found {% endif %} {% endfor %}

Mean profiles

Mean profiles not found

{% for i in range(conds|length) %} {% endfor %}
Condition DNA Signal Signal / DNA
Data 1st D 2nd D Data 1st D 2nd D Data 1st D 2nd D
{{conds[i].name}}
{% if cdescr|has_key(conds[i].name) %} {{i+1}} : {{cdescr[conds[i].name]}} {% endif %} 		Intercepts [x]
    {% for d in profeat[i]['dna'][0]['mean'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['mean'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['mean'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mean'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mean'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mean'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mean'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mean'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mean'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
Area [a.u.] {{profeat[i]['dna'][1]['mean']|round(3)}} {{profeat[i]['sig'][1]['mean']|round(3)}} {{profeat[i]['ratio'][1]['mean']|round(3)}}
{% if an_type == '3D' %}

Mean partial volume profiles

Mean partial volume profiles not found

{% endif %}

Median profiles

Median profiles not found

{% for i in range(conds|length) %} {% endfor %}
Condition DNA Signal Signal / DNA
Data 1st D 2nd D Data 1st D 2nd D Data 1st D 2nd D
{{conds[i].name}}
{% if cdescr|has_key(conds[i].name) %} {{i+1}} : {{cdescr[conds[i].name]}} {% endif %} 		Intercepts [x]
    {% for d in profeat[i]['dna'][0]['median'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['median'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['median'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['median'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['median'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['median'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['median'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['median'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['median'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
Area [a.u.] {{profeat[i]['dna'][1]['median']|round(3)}} {{profeat[i]['sig'][1]['median']|round(3)}} {{profeat[i]['ratio'][1]['median']|round(3)}}
{% if an_type == '3D' %}

Median partial volume profiles

Median partial volume profiles not found

{% endif %}

Mode profiles

Mode profiles not found

{% for i in range(conds|length) %} {% endfor %}
Condition DNA Signal Signal / DNA
Data 1st D 2nd D Data 1st D 2nd D Data 1st D 2nd D
{{conds[i].name}}
{% if cdescr|has_key(conds[i].name) %} {{i+1}} : {{cdescr[conds[i].name]}} {% endif %} 		Intercepts [x]
    {% for d in profeat[i]['dna'][0]['mode'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['mode'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['mode'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mode'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mode'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['mode'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mode'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mode'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['mode'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
Area [a.u.] {{profeat[i]['dna'][1]['mode']|round(3)}} {{profeat[i]['sig'][1]['mode']|round(3)}} {{profeat[i]['ratio'][1]['mode']|round(3)}}

Max profiles

Max profiles not found

{% for i in range(conds|length) %} {% endfor %}
Condition DNA Signal Signal / DNA
Data 1st D 2nd D Data 1st D 2nd D Data 1st D 2nd D
{{conds[i].name}}
{% if cdescr|has_key(conds[i].name) %} {{i+1}} : {{cdescr[conds[i].name]}} {% endif %} 		Intercepts [x]
    {% for d in profeat[i]['dna'][0]['max'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['max'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['dna'][0]['max'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['max'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['max'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['sig'][0]['max'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['max'][0] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['max'][1] %}
  • {{d|round(3)}}
    • {% endfor %}
    {% for d in profeat[i]['ratio'][0]['max'][2] %}
  • {{d|round(3)}}
    • {% endfor %}
Area [a.u.] {{profeat[i]['dna'][1]['max']|round(3)}} {{profeat[i]['sig'][1]['max']|round(3)}} {{profeat[i]['ratio'][1]['max']|round(3)}}
{% if an_type == '3D' %}

Mode partial volume profiles

Mode partial volume profiles not found

{% endif %}

DNA channel density profiles

mode, median, mean, max

{% for i in range(conds|length) %} DNA channel density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% if an_type == '3D' %}

DNA channel density profiles [partial volume]

mode, median, mean, max

{% for i in range(conds|length) %} DNA channel density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% endif %}

Signal channel density profiles

mode, median, mean, max

{% for i in range(conds|length) %} Signal channel density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% if an_type == '3D' %}

Signal channel density profiles [partial volume]

mode, median, mean, max

{% for i in range(conds|length) %} Signal channel density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% endif %}

Signal/DNA channels density profiles

mode, median, mean, max

{% for i in range(conds|length) %} Ratio density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% if an_type == '3D' %}

Signal/DNA channels density profiles [partial volume]

mode, median, mean, max

{% for i in range(conds|length) %} Ratio density scatter plot for condition '{{conds[i].name}}' not found. {% endfor %}

{% endif %}