Re: how to append results in excel file

Posted by Guy Lyons on Aug 02, 2017; 3:51am
URL: http://imagej.273.s1.nabble.com/how-to-append-results-in-excel-file-tp5002126p5019151.html

Thanks for the rapid reply, Brandon. I'm using Mac OsX 10.10.5, ImageJ 2.0.0-rc-43/1.51p. The macro as it stands has over 100 lines, so I'm not sure if it would be helpful to include it here. The macro currently is designed to analyse the output from a Cytation 3, which takes images of cell cultures in 3 channels from multiple areas of a culture vessel. There is a DAPI channel and 2 nuclear antigen-specific channels, and the Cytation software saves each channel in a separate file. Typically, 64 images are obtained per channel for each sample. The macro first uses the DAPI channel to create a mask to identify the nuclei and then uses a for loop to measure the area and the integrated density for each channel of each nucleus, writing the data for the area and each channel to a separate array, and then finally combining the arrays using Array.show and saving it as a csv. The macro does this for all of the Cytation 3 images in a folder. It does this successfully and reasonably quickly, writing the data to a csv file for each image. We (i.e. my student) then manually combine the data from the 64 csv files by copying and pasting within Excel – a tedious task that includes the possibility of making mistakes.

The strategies that I have tried in order to generate a single file (including some based on the links that you sent) by modifying the for loop run into the problem of having to write to the Results window but also having to "Clear Results" between analysis of channels (each channel being recorded in a separate original file). The simplest solution for me would be a method that combines the data of multiple csv files into a single csv file with just one row of headers. Maybe someone out there can accept this as a challenge? I'm sure I'm not the only one who would find it useful.

Guy.

Brandon Hurr wrote

Depends how you're doing your analysis.

If you're looping through pictures in a folder then you should create a
results table and print to that in every iteration. I typically save the
results table to a file every loop too in case of problems. You can just
overwrite this every iteration rather than append (writing a csv file is
not that time consuming unless the file is huge).

If you're doing something else... you'll have to spell that out and help us
help you (and others).

How to make a custom results table and record to it:
http://imagej.1557.x6.nabble.com/How-to-create-a-customised-results-table-and-add-data-to-it-within-a-macro-td5000701.html
Save that file out as csv (txt):
http://imagej.1557.x6.nabble.com/save-results-table-as-csv-with-custom-name-td5003427.html

Put that into a loop and you're golden.

B

On Tue, Aug 1, 2017 at 7:15 PM, Guy Lyons <[hidden email]> wrote:

> I am trying to do exactly what Annie Venien described in the original post
> using ImageJ macro language i.e. save analysis data from images into
> individual files AND also combine them into a single csv file. Tried all
> sorts of things involving strings, File.append, etc., to combine them into
> a
> single csv file, but can't crack it. A lot of people have requested advice
> for the same thing in various forums. The "Read and Write Excel" plugin
> adds
> data side-by-side, instead of appending it in columns. Has anyone come up
> with a plugin or other method to achieve this, either as you go during
> analysis of multiple files, or post-analysis to concatenate csv data files
> vertically?
>
>
>
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