All reports will open a table of text that can be copy/pasted into another program for further analysis.

There are three types of reports: stack reports, segment reports, and map reports.

Stack Reports

Reports can be generated directly from each stack window.

Tip. Use keyboard '[' in any stack window to open and close the left stack db panel.

Line Segments

  • Keyboard ‘e’ In the ‘Line Segments’ section of the main stack db panel to display a summary of each segment.
  • Keyboard ‘E’ In the ‘Line Segments’ section of the main stack db panel to display the entire line (all 3D points)

Points (stack db)

  • Keyboard ‘e’ In the ‘Points’ section of the main stack db panel to display the stack db as a table.
  • Keyboard ‘i’ In the ‘Points’ section of the main stack db panel to display intensity analysis as a table.

Segment Reports

Segment Report

A segment report display statistics for each segment in a stack. It displays the length of the segment, the number and density of spines, the x/y/z position of the segment, and the number of each user spine type (e.g. mushroom, stubby, etc.). A segment report can be generated for individual stacks or a map.

To generate a segment report for each segment in a stack

  • In a stack window, keyboard ‘o’ for output report.
  • In the Stack Browser, select a stack in the list, keyboard ‘o’ for output report.
  • In the Stack Browser, right click a stack in the list of stacks and select ‘Segment Report’.
  • In the Stack Browser, right click a folder in the list folders (on the left) and select ‘Segment Report (All Stack)’.

The columns in a segment report are as follows

Name Meaning
numSpines Total number of spines = goodSpines + badSpines
goodSpines Number of good spines.
badSpines Number of bad spines.
totalLen (2D) Total segment length (um)
goodLen (2D) Segment length (um) from most distal good spines.
totalDen (2D) Total density of all spines = numSpines / totalLen
goodDen (2D) Density of good spines = goodSpines / goodLen
totalLen3d (3D)
goodLen3d (3D)
totalDen3d (3D)
goodDen3d (3D)
zMin  
zMax  
zMean  
zMedian  
zAngle  
xyAngle  
tort  
xMin  
xMax  
xMean  
xMedian  
yMin  
yMax  
yMean  
yMedian  
nUnknown Number of spines with userType ‘Unknown’
nMushroom Number of spines with userType ‘Mushroom’
nFilapodia Number of spines with userType ‘Filapodia’
nLong Number of spines with userType ‘Long’
nStubby Number of spines with userType ‘Stubby’

Map Reports

There are two types of map reports, Dynamics and Survival. Each report begins with a header that gives information about each session in the report

Name Meaning
Idx Session Index
Map Name of the map
sessCond Session Condition
mapSegment Map specific segment index (different from stackSegment)
Stack Name of the stack (used internally)
originalFile Original file name of the stack
stackSegment Stack specific segment index (different from mapSegment)
date The date the stack was acquired
time The time the stack was acquired
seconds The seconds the stack was acquired (from 12:00 AM on Jan 1, 1904)

Dynamics Report

A dynamics report is used for a map. For each session in a map, it will calculate the length of each segment (um), the number of added and subtracted spines, the density of added and subtracted spines, etc. etc.

In any map plot, right-click and select ‘Dynamics Report’. If the map plot is displaying ‘All Segment’, a table for each segment will be opened. Otherwise, one table for the current ‘Map Segment ID’ will be opened.

The report is broken into different sections.

Information about the segment tracing
Name Meaning
totalLen2d Total 2D length of tracing (um)
goodLen2d 2D length of tracing between most distal ‘good’ objects (um)
smoothPoints Boxcar smoothing for tracing z (0 means no smoothing)
totalLen3d The smoothed total 3D length of tracing (um)
goodLen3d The smoothed 3D length of tracing between most distal ‘good’ object (um)
Information about all object (ignoring user type)
Name Meaning
density density = nTotal / goodLen3d
nTotal Total number of spines (is same as nGood + nBad)
nGood Total number of good spines
nBad Total number of bad spines
   
nAdd Number of added spines.
nSub Number of subtracted spines (at the current session)
nSub2 Number of subtracted spines (from the previous session)
   
pAdd Percent added = nAdd / nGood from previous session * 100
pSub Percent subtracted = nSub / nGood from previous session * 100
pSub2  
   
dAdd Density added = nAdd / goodLen3d from previous session
dSub Density subtracted = nSub / goodLen3d from previous session
dSub2  
Information about user type 0
Name Meaning
density_ut0 Density of user type 0 = nTotal_ut0 / googLen3d
nTotal_ut0 Total number of user type 0
nGood_ut0 Total number of good user type 0
nBad_ut0 Total number of bad user type 0
   
nAdd_ut0 Number of added user type 0
nSub_ut0 Number of subtracted user type 0
nSub2_ut0  
   
pAdd_ut0 Percent of added user type 0 = nAdd_ut0 / nGood_ut0 from previous session *100
pSub_ut0 Percent of subtracted user type 0 = nSub_ut2 / nGood_ut0 from previous session
pSub2_ut0  
   
dAdd_ut0 Density of added user type 0 = nAdd_ut0 / goodLen3d from previous session
dSub_ut0 Density of subtracted user type 0 = nSub_ut0 / goodLen3d from previous session
dSub2_ut0  
Information about user type 1, 2, 3, … 5

Other sections will be appended to the report to give information about ‘user type 1’, ‘user type 2’, ‘user type 3’, …, ‘user type 5’

Survival Report

A survival report calculates the number of objects remaining from an initial ‘seed’ session. Like a Dynamics report, it breaks down objects into different sections including all objects, followed by user type 0, followed by user type 1, etc. etc.

Information about all object (ignoring user type)
Name Meaning
surv_all_s0 For each session, the number of surviving objects relative to seed session 0
psurv_all_s0 For each session, the fraction of surviving objects relative to seed session 0
  Note: This can continue with different seed sessions, for example, surv_all_s2 would give the number of surviving objects relative to seed session 2
Information about user type 0
Name Meaning
surv_type0_s0 For each session, the number of surviving user type 0 objects relative to seed session 0
psurv_type0_s0 For each session, the fraction of surviving user type 0 objects relative to seed session 0
  Note: This can continue with different seed sessions, for example, surv_type0_s2 would give the number of surviving user type 0 objects relative to seed session 2
Information about user type 1
Name Meaning
surv_type1_s0 For each session, the number of surviving user type 1 objects relative to seed session 0
psurv_type1_s0 For each session, the fraction of surviving user type 1 objects relative to seed session 0
Information about user type 2, 3, 4, 5

Other sections will be appended to the report to give information about ‘user type 2’, ‘user type 3’, ‘user type 4’ and ‘user type 5’