Format problem when ExporttoSpreedsheet

Hi,

I tried many times on my own pipeline and the examples from CellProfiler as well, but the problem remained. After ExporttoSpreedsheet, all the data is always stuffed into the A column. Could you help me?

Another question is that if I want to directly obtain the diameter instead of the area of circular speckles, how should I set the parameters in CellProfiler?

The last quesion is that can CellProfiler process .DAT file (text image) directly? Currently I am doing it in this way:

Export the images from the microscope software as .DAT;
Import as “text image” in Image J and then resize;
Batch process in DeconvolutionLab (a plugin)
Batch convert to 8 bit .TIF;
Analyze in CellProfiler…

I wonder if there is some better way to do it?

Many thanks for your time and help in advance!
Brian


Are you using .csv as the spreadsheet extension? If not, Excel may not be properly recognizing what the file format actually is and treat it accordingly. Alternately, you can try the Text Import Wizard in Excel.

You can use the MajorAxisLength measure from MeasureObjectSizeShape as a surrogate for the diameter. For circular objects, they evaluate to the same measure; for non-circular objects, the major axis is the length of the longest object axis.

CellProfiler uses Bio-Formats to read image data, and it appears that text images are supported by Bio-Fomats (although they would need to have the extension .txt). However, this extension is not currently enabled in CellProfiler.

Also, you are performing additional pre-processing steps prior to creating the final TIFs; resizing is doable in CellProfiler but deconvolution is not a CellProfiler function. Given those limitations, it seems that the approach you have taken is a good one.

Cheers,
-Mark

Good! It did work well with Text Import Wizard! Thanks!

Good! BTW, Is the MajorAxisLength the same as “Feret’s diameter” in Image J?

Good! Thanks!

May I ask a new question? I have two channels so two images with regards to a cell. One image (A) is to define the area and the shape of a cell. Another image (B) is full of speckles. If I want to use (A) to find the center of the cell, and then get a distribution of the distance of the speckles relative to the center (or border/periphery, same) of the cell, Can CellProfiler do it?
I thought of finding the local mixima of the speckles and then the distance to the cell center;
I also thought that a radial distribution of the intensity also gives the meaning, but just that the cell shape is irregular and the radial distribution usually works with retangular, circular or ellipse shape?

They’re actually different. You can see a definition of major axis length here, as compared to Feret’s diameter here.

You may want to check into the RelateObjects module. One of the options of this module is to calculate distances from sub-objects to the centroid or perimeter of the enclosing object.

Hope this helps!
-Mark