Query about/Suggestion for an add to Results.txt in measurements

[Denny Hugg]

In four weeks of testing, I have become convinced of the accuracy and speed advantage in measuring trematode images using ImageJ or Fiji. The only complicating factor in the tools' use is the necessity to either restrict measurement data collection to a single ROI or to use long and detailed filenames when saving "Results.txt" to adequately define and describe each data element collected.

We who must repetitively measure preserved or live biological specimens often rely on checklists to prompt us of measurement sequences and to receive recorded data when "Results.txt" cannot adequately describe our sequences of measurements. Two such checklist examples follow this text.

Is there, or could there be, a plugin which would read line-at-a-time from a measurement sequence text file such as below, and place the text into the lead field of "Results.txt" in preparation to record data from the upcoming measurement? Such an adjunct to use of ImageJ-Fiji would enable creation of complicated measurement sequences without potential data loss or errors due to confusion of field identities. Likely it is that someone has already done this. Where might one find the plugin or macro? If the time for this is not yet, how could I be of help, realizing my unfamiliarity with ImageJ plugin writing, to try to attain this Cadillac of trematode image measuring tools?

Warm regards,

Denny Hugg
Gulf Coast Research Lab, Parasitology
Ocean Springs, MS

Example #1 TREMATODE WHOLE BODY MEASUREMENTS
"Collection Record Number"
"Specimen"
"Body length"
"Body width"
"W/L"
"Genital pore to anterior end"
"Ventral sucker to anterior end"
"ventral sucker to posterior end"
"Cecal bifurcation to anterior end"
"Ceca to posterior end"
"Oral sucker length"
"Oral sucker width"
"Ventral sucker length "
"Ventral sucker width"
"Prepharnnx length"
"PH to pre"
"Pharynx length"
"Pharynx width"
"Esophagus"
"Ovary to ventral sucker"
"OV to ve"
"Testis length"
"Testis width"
"Ovary length"
"Ovary width"
"Vitelline to ventral sucker"
"Vitelline to posterior end"
"post vit"
"Hermaphroditic sac length"
"Hermamroditic sac width"
"Internal seminal vesicle length"
"Internal seminal vesicle width"
"External seminal vesicle length"
"External seminal vesicle width"
"testis to ovary"
"testis to ventral sucker"
"testis to posterior end"
"post test"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"


Example #2 STRIGEID TREMATODE FOREBODY MEASUREMENTS
LENFB - length to lwr midpt of tribocytic organ
WIDFB - width @ max forebody
STRIC - width @ body stricture
LENOS - length of oral sucker
WIDOS - width of oral sucker
LENPH - lengt of pharynx
WIDPH - width of pharynx
LENES - length of esophagus (PH to fork)
LENVS - length of ventral sucker
WIDVS - width of ventral sucker
LENTR - anterior edge to lwr apex
WIDTR - width tribocytic organ max
LLNTR - longest length of TR ant-lwr extr

[Krs5]

Dear Denny,

I put your lists in header list.txt and header list2.txt resp and wrote two macros to make these lists headers of a results table. The only thing I could not get working is how to make it a header of an empty table. I used setResults what wants a table value for each header entry. Does somebody has an idea how to avoid this?

macro Header_test1{  
        selectWindow("header list.txt");
  table = getInfo();
  rows = split(table, "\n");
  for (i=1; i<rows.length; i++) {
                rows[i]=substring(rows[i],1);
                rows[i]=substring(rows[i],0,lengthOf(rows[i])-1);
                setResult(rows[i],0,0);
        }
}

macro Header_test2{
        answer1 = false;
        answer2 = false;
        space=" ";
        selectWindow("header list2.txt");
        table = getInfo();
        rows = split(table, "\n");
        for (i=0; i<rows.length; i++) {
                values = split(rows[i]);
                for (j=0; j<values.length; j++){
                        if(answer2 == true){
                                if (answer1 == false){
                                        header = values[j];
                                        header = header + space;
                                        answer1 = true;
                                }else{
                  word=values[j];
                                        if (word=="-"){
                                                setResult(header,0,0);
                                                answer1=false;
                                        }else{
                                                header = header + word;
                                                header = header + space;
                                        }
                                }
                        }
                        word=values[j];
                        if (word=="-") answer2=true;
                }
        }
}

Cheers

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology
University of Leicester

http://www.le.ac.uk/biochem/microscopy/home.html



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Denny Hugg
Sent: 15 February 2012 15:46
To: [hidden email]
Subject: Query about/Suggestion for an add to Results.txt in measurements

In four weeks of testing, I have become convinced of the accuracy and speed advantage in measuring trematode images using ImageJ or Fiji. The only complicating factor in the tools' use is the necessity to either restrict measurement data collection to a single ROI or to use long and detailed filenames when saving "Results.txt" to adequately define and describe each data element collected.

We who must repetitively measure preserved or live biological specimens often rely on checklists to prompt us of measurement sequences and to receive recorded data when "Results.txt" cannot adequately describe our sequences of measurements. Two such checklist examples follow this text.

Is there, or could there be, a plugin which would read line-at-a-time from a measurement sequence text file such as below, and place the text into the lead field of "Results.txt" in preparation to record data from the upcoming measurement? Such an adjunct to use of ImageJ-Fiji would enable creation of complicated measurement sequences without potential data loss or errors due to confusion of field identities. Likely it is that someone has already done this. Where might one find the plugin or macro? If the time for this is not yet, how could I be of help, realizing my unfamiliarity with ImageJ plugin writing, to try to attain this Cadillac of trematode image measuring tools?

Warm regards,

Denny Hugg
Gulf Coast Research Lab, Parasitology
Ocean Springs, MS

Example #1 TREMATODE WHOLE BODY MEASUREMENTS
"Collection Record Number"
"Specimen"
"Body length"
"Body width"
"W/L"
"Genital pore to anterior end"
"Ventral sucker to anterior end"
"ventral sucker to posterior end"
"Cecal bifurcation to anterior end"
"Ceca to posterior end"
"Oral sucker length"
"Oral sucker width"
"Ventral sucker length "
"Ventral sucker width"
"Prepharnnx length"
"PH to pre"
"Pharynx length"
"Pharynx width"
"Esophagus"
"Ovary to ventral sucker"
"OV to ve"
"Testis length"
"Testis width"
"Ovary length"
"Ovary width"
"Vitelline to ventral sucker"
"Vitelline to posterior end"
"post vit"
"Hermaphroditic sac length"
"Hermamroditic sac width"
"Internal seminal vesicle length"
"Internal seminal vesicle width"
"External seminal vesicle length"
"External seminal vesicle width"
"testis to ovary"
"testis to ventral sucker"
"testis to posterior end"
"post test"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"
"Egg Length"
"Egg Width"


Example #2 STRIGEID TREMATODE FOREBODY MEASUREMENTS
LENFB - length to lwr midpt of tribocytic organ
WIDFB - width @ max forebody
STRIC - width @ body stricture
LENOS - length of oral sucker
WIDOS - width of oral sucker
LENPH - lengt of pharynx
WIDPH - width of pharynx
LENES - length of esophagus (PH to fork)
LENVS - length of ventral sucker
WIDVS - width of ventral sucker
LENTR - anterior edge to lwr apex
WIDTR - width tribocytic organ max
LLNTR - longest length of TR ant-lwr extr

[Sand Roader]

Thank you, Dr. Straatman. I will study this approach and if I can ad
anything of value (doubtful), I will.

I deeply appreciate your interest.

Denny Hugg
Volunteer Parasitologist
Gulfport, MS USA

On Fri, Feb 17, 2012 at 12:18 PM, Straatman, Kees R. (Dr.) <
[hidden email]> wrote:

> Dear Denny,
>
> I put your lists in header list.txt and header list2.txt resp and wrote
> two macros to make these lists headers of a results table. The only thing I
> could not get working is how to make it a header of an empty table. I used
> setResults what wants a table value for each header entry. Does somebody
> has an idea how to avoid this?
>
> macro Header_test1{
>        selectWindow("header list.txt");
>         table = getInfo();
>         rows = split(table, "\n");
>         for (i=1; i<rows.length; i++) {
>                rows[i]=substring(rows[i],1);
>                rows[i]=substring(rows[i],0,lengthOf(rows[i])-1);
>                setResult(rows[i],0,0);
>        }
> }
>
> macro Header_test2{
>        answer1 = false;
>        answer2 = false;
>        space=" ";
>        selectWindow("header list2.txt");
>        table = getInfo();
>        rows = split(table, "\n");
>        for (i=0; i<rows.length; i++) {
>                values = split(rows[i]);
>                for (j=0; j<values.length; j++){
>                        if(answer2 == true){
>                                if (answer1 == false){
>                                        header = values[j];
>                                        header = header + space;
>                                        answer1 = true;
>                                }else{
>                                        word=values[j];
>                                        if (word=="-"){
>                                                setResult(header,0,0);
>                                                answer1=false;
>                                        }else{
>                                                header = header + word;
>                                                header = header + space;
>                                        }
>                                }
>                        }
>                        word=values[j];
>                        if (word=="-") answer2=true;
>                }
>        }
> }
>
> Cheers
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> College of Medicine, Biological Sciences and Psychology
> University of Leicester
>
> http://www.le.ac.uk/biochem/microscopy/home.html
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Denny Hugg
> Sent: 15 February 2012 15:46
> To: [hidden email]
> Subject: Query about/Suggestion for an add to Results.txt in measurements
>
> In four weeks of testing, I have become convinced of the accuracy and
> speed advantage in measuring trematode images using ImageJ or Fiji. The
> only complicating factor in the tools' use is the necessity to either
> restrict measurement data collection to a single ROI or to use long and
> detailed filenames when saving "Results.txt" to adequately define and
> describe each data element collected.
>
> We who must repetitively measure preserved or live biological specimens
> often rely on checklists to prompt us of measurement sequences and to
> receive recorded data when "Results.txt" cannot adequately describe our
> sequences of measurements. Two such checklist examples follow this text.
>
> Is there, or could there be, a plugin which would read line-at-a-time from
> a measurement sequence text file such as below, and place the text into the
> lead field of "Results.txt" in preparation to record data from the upcoming
> measurement? Such an adjunct to use of ImageJ-Fiji would enable creation of
> complicated measurement sequences without potential data loss or errors due
> to confusion of field identities. Likely it is that someone has already
> done this. Where might one find the plugin or macro? If the time for this
> is not yet, how could I be of help, realizing my unfamiliarity with ImageJ
> plugin writing, to try to attain this Cadillac of trematode image measuring
> tools?
>
> Warm regards,
>
> Denny Hugg
> Gulf Coast Research Lab, Parasitology
> Ocean Springs, MS
>
> Example #1 TREMATODE WHOLE BODY MEASUREMENTS
> "Collection Record Number"
> "Specimen"
> "Body length"
> "Body width"
> "W/L"
> "Genital pore to anterior end"
> "Ventral sucker to anterior end"
> "ventral sucker to posterior end"
> "Cecal bifurcation to anterior end"
> "Ceca to posterior end"
> "Oral sucker length"
> "Oral sucker width"
> "Ventral sucker length "
> "Ventral sucker width"
> "Prepharnnx length"
> "PH to pre"
> "Pharynx length"
> "Pharynx width"
> "Esophagus"
> "Ovary to ventral sucker"
> "OV to ve"
> "Testis length"
> "Testis width"
> "Ovary length"
> "Ovary width"
> "Vitelline to ventral sucker"
> "Vitelline to posterior end"
> "post vit"
> "Hermaphroditic sac length"
> "Hermamroditic sac width"
> "Internal seminal vesicle length"
> "Internal seminal vesicle width"
> "External seminal vesicle length"
> "External seminal vesicle width"
> "testis to ovary"
> "testis to ventral sucker"
> "testis to posterior end"
> "post test"
> "Egg Length"
> "Egg Width"
> "Egg Length"
> "Egg Width"
> "Egg Length"
> "Egg Width"
> "Egg Length"
> "Egg Width"
>
>
> Example #2 STRIGEID TREMATODE FOREBODY MEASUREMENTS
> LENFB - length to lwr midpt of tribocytic organ
> WIDFB - width @ max forebody
> STRIC - width @ body stricture
> LENOS - length of oral sucker
> WIDOS - width of oral sucker
> LENPH - lengt of pharynx
> WIDPH - width of pharynx
> LENES - length of esophagus (PH to fork)
> LENVS - length of ventral sucker
> WIDVS - width of ventral sucker
> LENTR - anterior edge to lwr apex
> WIDTR - width tribocytic organ max
> LLNTR - longest length of TR ant-lwr extr
>