Input Panel

LM uses swc format natively for processing the data or for swc conversions. The original reference for SWC format is described here by its inventor, Robert Cannon.
More information related to SWC format including the convention followed for arbor type description is found here:
http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
http://research.mssm.edu/cnic/swc.html

Input Panel allows you to select and add one or more input neuron file(s) to be analyzed.
- A single input neuron
- Multiple input neurons as shown the figure below
- A whole directory that has a valid set of reconstruction files.

Click on the Add button to select files or directory containing files from your local disks via a file chooser dialog box.
The selected files are shown in the text area. Selected files can be removed using the 'Remove' button.
'Remove All' button removes all the files from the text area.



For a standard morphological functional analysis, it is sufficient to select files in the Group1 window. As you can see from the figure above.

However, if you are doing a stat_test then you should check the Stat_tests check box and select Group2 files also. Please see the how to do stat test manual


Input File Format

Supported formats include:

SWC Format # Amaral to SWC conversion from L-Measure. R. Scorcioni: rscorcio@gmu.edu
# Original fileName:C:\\cells\\ca1\\Amaral\\C8076E.txt
#
1 1 -12 -25.7308 5.19231 4.1729 -1
2 10 0 0 0 0.5 1
3 2 -13 -32.5 2 0.4 2
4 2 -14 -43 5 0.4 3
5 2 -11.5 -50.5 9 0.2 4
Neurolucida Format ; V3 text file written for MicroBrightField products.
(Sections S1 "Section 1" 15 15 0
S2 "Section 2" 0 30 0
S3 "Section 4a" -55 25 0
S4 "Section 3a" -30 25 0
S5 "Section 5" -80 25 0
) ; End of Sections

("CellBody"
(Color Red)
(CellBody)
( 21.84 -19.47 -10.75 0.22 S2) ; 1, 1
( 20.25 -18.17 -10.75 0.22 S2) ; 1, 2
Amaral Format No. points 1722 No. trees 10
Text File sent from PDP-11

Point Type Tag X Y Z Thick Name Attachment

1 MTO 0 -4.0 -21.0 7.0 4.3 da1 ------ 0
2 CP 0 -4.0 -25.5 7.0 4.0
3 CP 0 -1.0 -35.0 6.5 2.7
4 CP 0 -.5 -40.5 8.0 2.4
Burke Format  
Claiborne Format /*
DIG version 5.19 3-28-89 Rocky Nevin
Comments: Cell went in well. All branches accounted for. In on 11-13-90.
*/
1 S -0.79 1.83 1.47 5.86
2 S -2.65 3.63 2.78 9.91
3 S -3.71 5.88 2.28 13.52
4 S -0.79 9.71 2.78 10.36
5 S 0.79 12.19 -0.23 8.11
6 S 2.38 14.44 1.84 7.21
7 P 3.18 16.92 1.54 5.86
Eutectic Format No. points 583
No. trees 6
Text CTMZ0791.GE1, Mudpuppy, HRP in eyecup 15 minutes.

Point Type Tag X Y Z Thick Name Attachment

1 SOS 0 .0 -2.0 .0 .1 ------
2 SCP 0 .0 -4.0 .0 .1
3 SCP 0 2.0 -5.5 .0 .1
4 SCP 0 3.5 -7.0 .0 .1
5 SCP 0 5.5 -8.5 .5 .1
6 SCP 0 8.5 -9.0 .5 .1
Amira Format
 
# AmiraMesh ASCII 1.0
# Created by WriteNeuronToAM -  2007-05-09 17:46:36 BST 

define Lines 245 
define Vertices 188 

Parameters {
    ContentType "HxLineSet"
}

Vertices { float[3] Coordinates } = @1
Vertices { float Data } = @2
Lines { int LineIdx } = @3

@1 #  188 xyz coordinates
30.49623842616 -87.78503774352 -41
32.47941327644 -86.62928021488 -42
34.12111431144 -85.47352268624 -43

...

@2 # 188 width values
0.815
0.815
0.69

...

@3 # 245 line segements
0 1 2 3 4 5 6 7 8 9 10 11 12 -1 
12 13 -1 
13 14 15 16 -1 

...

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