How to use APP with siMPle

1. Load or convert the files

.spe, or .dmd, .dx, etc.

2. Load the reference file

For AWI analysis: siMPle_automated_analysis_library_VersionX.txt

It is available on the Downloads page

Please keep in mind that the reference data was measured in absorbance and press OK

3. It should now look like this:

4. Please check user setup -> options

And adjust to these values and options:

And generate a project file, here "How to" and click save.

6. Wait until the calculations are finished

7. Afterwards, click on the button "Save to pipeline"

8. Chose a file name

Take care not to rename the database file (currently it is the default name generated by siMPle):

Saving the file may take a while.

9. Open the APA.exe or MPAPP.exe

(Both filenames contain also the current version number as eg. APAv1.01.exe, which may differ due to updates) depending on the pipeline you want to use.
The files are available here

10. After a short while the user interface shows up:

11. Please set the pixelsize

to the value of your system, here 11.03, and press Set Pixelsize (otherwise 11.14 will be used as default).

12. By pressing “file name” you can chose the generated file

Here HowTo.txt in the “MPhunter Agilent” folder

13. Choose a result folder by pressing “result dir”

Here APA in the “MPhunter Agilent” folder.

This folder needs to be in the same folder as the executable and currently no subfolders are allowed (known bug, work in progress).

After all folders, files and settings are set

14. Please press Analyse from MPhunter

to start the analysis of the generated data followed by Image Analysis.

The start should look like this:

15. Finished analysis:

15. The generated data contains various different files including all data and images generated during image analysis:

a.) A histogram for polymer type hits based on spectra.

b.) The combined (_closed_image.csv) and the individual (_closed_imageID.csv, ID = 01, etc.) image files.

c.) The number of particles found for each pixel area (_particle_histogramID.csb)

d.) All individual particle information (which number has which size) as _individualID.csv.

e.) A histogram for polymer type hits based on particle (_particles_perpolymer.csv)

f.) The size classes used in various publication:

_sizeclassesID.csv for individual particles types,

_bio for natural materials,

_polymer for plastic materials,

_other for all other materials,

_bulk (bio, polymer and other combined),

_forcalculations (all individual sizeclasses in one file):

Data reads as followed (the first column label with "s" is not containing data and needs has be skipped for calculations):

   _forstatistics (all individual sizeclasses in one file):)

g.) Greyscale image of the raw and final images.

17. Welcome to the data Jungle! Analysis finished!

18. Troubleshooting:

a.) Error Messages (Traceback):

     i.) Missing the threshold.csv file in the folder with the executable for APA/MPAPP: