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Table 1 Metrics automatically collected and derived from the image data, as stored tabularly in the HDF5 file

From: mycelyso – high-throughput analysis of Streptomyces mycelium live cell imaging data

Level

Metric

Fits

Per position and time

Image dimensions

 
 

Crop values

 
 

Covered area

Linear/logarithmic1, raw/optimized2

 

Total mycelium length

Linear/logarithmic1, raw/optimized2

 

Branching point count

Linear/logarithmic1, raw/optimized2

 

Tip count

Linear/logarithmic1, raw/optimized2

Per hypha track

Start/mid/end time point

 
 

Duration spanned

 
 

Count of time points spanned

 
 

Minimum/maximum length

 
 

Minimum/maximum node hop count

 

Per hypha and time

Time point

 
 

Length

Absolute/relative3, Linear/logarithmic1, Raw/optimized2

 

Node identifiers

 
 

Distance in node hops

 
 

Node identifiers of the successor segment

 
  1. 1Logarithmic fit: data are transformed by taking the natural logarithm and fitted with linear regression
  2. 2Optimized fit: data are fitted within the widest continuous support with R2>0.9
  3. 3Relative length: length measurement is taken relative to the minimum hypha length of the track