The particle measure

From Endrov

(Redirected from Flow ParticleMeasure)

Once you have segmented your image, you can use the Particle measure to quantify your segmented objects.

Contents

Usage

You are assumed to have two channels: One is a mask (segmentation) of your image, the other is the original image itself. See previous tutorials. The basic connection looks like this:

usingparticlemeasure3.png

The particle measure does not want your mask - rather it wants an image where each pixel is an ID of the particle it belongs to. This can be generated from your mask using the flow object identify particles (view it in the image view to get an ID of what happens). Then take the ID image and the original image and measure it. The object allows you to specify which attributes you want to extract.

To view the particle measure, you can either create a raw table in the flow, but better is to store it down in a new object and use the plate analysis window.

Storage

If you do not want to use the plate analysis window, you can choose to instead store it down directly in SQL or in a CSV file. You then just add any of these objects to your flow:

CSV

CSV can be imported in most spreadsheet programs e.g. OpenOffice. The character between columns can be changed but tabs are usually good.

Pm2csv.png

SQL

To use SQL you first have to set up a server. PostgreSQL is recommended, MySQL less so. Any JDBC-compliant SQL database can be used. You may have to drop new .jar-files into the libs/-directory, see the instructions for your database (let us know if you have problems). You have to create a new database yourself, and from that you will know the URL, user and password. The dataid parameter is used to store the output of multiple recordings in the same table; there will be a separate dataid column that can be used to distinguish them.

There are buttons to manually interact with the database. You need not bother with these normally (you have to execute before they work) unless you change which parameters are extracted.

Pm2sql.png