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FlowCAM color plugin
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Hello,
Some months ago I tried to process samples from a colour FlowCAM with the FIT_VIS plugin for ImageJ in order to use ZooPhytoImage later. The plugin did not work and I thought the problem was that the images were RGB and not greyscale.
But, in fact, the plugin is prepared to change colour images to greyscale images and work with them (it is not of great importance to lost colour information since colour images are not calibrated, calibration images are greyscale (!!)).
So, I realized the problem was in the software version because from VisualSpreadsheet 1.5.14 to current versions there have been some minor changes in Contexts fields and Data headers.
Now I have changed my mind and I am doing the same job with R (EBImage package) which is a code I am more familiar with, but, maybe, it could be useful for somebody to know what changes must be done in the FIT_VIS plugin to work with FlowCAM samples obtained with VisualSpreadsheet 2.0.0 or later.
About Context fields: SaveIntervalMinutes has changed to RecalibrationIntervalMinutes:
Line 558
/** this method populated the Cal_Filename field based upon time */
private boolean alignCalFiles(String[] calFiles){
//make sure we are ready to access data
if (dataAsArray==false){splitVector(",", vData);}
//calibration interval in minutes -> converted to mS
long dCal = parseLong(getValue("RecalibrationIntervalMinutes", vCtx));
dCal = dCal * (long) 60000;
About Data Headers: some new variables have been included and other ones have changed their name, so they must be listed as follows, in this case it is not necessary to delete the previous ones, because as the header says it is a list of possible data fieldnames:
Line 1456
/** populates the possible data file fieldnames and field types
this is just a look up table of known combinations */
private boolean populatedataflags(){
vDataFlags.add("Id=INT32");
vDataFlags.add("Area_ABD=FLOAT32");//was Area (ABD)
vDataFlags.add("Diameter_ABD=FLOAT32");
vDataFlags.add("Volume_ABD=FLOAT32");
vDataFlags.add("Diameter_ESD=FLOAT32");
vDataFlags.add("Volume_ESD=FLOAT32");
vDataFlags.add("Length=FLOAT32");
vDataFlags.add("Width=FLOAT32");
vDataFlags.add("Aspect_Ratio=FLOAT32");
vDataFlags.add("Transparency=FLOAT32");
vDataFlags.add("Intensity=FLOAT32");
vDataFlags.add("Sigma_Intensity=FLOAT32");
vDataFlags.add("Sum_Intensity=FLOAT32");
vDataFlags.add("Compactness=FLOAT32");
vDataFlags.add("Elongation=FLOAT32");
vDataFlags.add("Perimeter=FLOAT32");
vDataFlags.add("Convex_Perimeter=FLOAT32");
vDataFlags.add("Roughness=FLOAT32");
vDataFlags.add("Feret_Max_Angle=FLOAT32");
vDataFlags.add("Feret_Min_Angle=FLOAT32");
vDataFlags.add("PPC=FLOAT32");
vDataFlags.add("Ch1_Peak=FLOAT32");
vDataFlags.add("Ch1_Peak_Area=FLOAT32");
vDataFlags.add("Ch2_Peak=FLOAT32");
vDataFlags.add("Ch2_Peak_Area=FLOAT32");
vDataFlags.add("Ch3_Peak=FLOAT32");
vDataFlags.add("Ch3_Peak_Area=FLOAT32");
vDataFlags.add("Ch2/Ch1_Ratio=FLOAT32");
vDataFlags.add("Edge_Gradient=FLOAT32");
vDataFlags.add("Avg_Red=FLOAT32");
vDataFlags.add("Avg_Green=FLOAT32");
vDataFlags.add("Avg_Blue=FLOAT32");
vDataFlags.add("Ratio_Red_Green=FLOAT32");
vDataFlags.add("Ratio_Blue_Green=FLOAT32");
vDataFlags.add("Ratio_Red_Blue=FLOAT32");
vDataFlags.add("CaptureX=INT32");
vDataFlags.add("CaptureY=INT32");
vDataFlags.add("SaveX=INT32");
vDataFlags.add("SaveY=INT32");
vDataFlags.add("PixelW=INT32");
vDataFlags.add("PixelH=INT32");
vDataFlags.add("Cal_Const=FLOAT32");
vDataFlags.add("Timestamp=STRING");
vDataFlags.add("Filename=STRING");
vDataFlags.add("Filter_Score=FLOAT32");
vDataFlags.add("Source_Image=FLOAT32");
vDataFlags.add("Cal_Filename=STRING");
vDataFlags.add("Calibration_Image=FLOAT32");
vDataFlags.add("UClass=INT32");
vDataFlags.add("UConf=INT32");
vDataFlags.add("UComment=STRING");
Well, these are all changes I found and modifying them the plugin works correctly (the macro FIT_VIS.txt does not need to be modified). But changes in the same way could be done in the future software updates.
Best,
Eva
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Hi Eva,
Thanks for the info and suggestions. You have bumped into the same issues we have all struggled with regarding FlowCAM - that the data format/contents change between successive versions. While FIT has come a long way toward making the data readily available to for post-processing, there are still the little things that you discovered that can and will break third-party software like the FIT_VIS plugin.
Kevin and I have worked with this very issue a lot last winter and spring. In the end we decided to change the plugin's operating paradigm so that ImageJ (and the plugin for FlowCAM) require minimal input from the user and that the context file is not mined for data at all. In the background, R is used to prep the data for input into the plugin and for assembling the data after processing for use in ZooImage. Unfortunately, the updated plugin is not ready release just yet.
In the meantime, it looks like you have a nice solution.
Cheers,
Ben
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Hi Ben and Eva,
I'm now working on the same kind of problem as you were almost one year ago according to those posts.
I tried to use the FIT VIS plugin with ImageJ on my Flowcam files (color) but it doesnt work. I will try the changes given by Eva...But I would also like to know if the new plugin you were talking about, Ben, is now ready for release....
Any comments or help on that subject would be much appreciated!!
cheers
Elise
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Hi,
Goodness! You have been very patient.
Development has been sporadic but I think it could be made available by the end of the month. I'll squeak when I have it.
Cheers,
Ben
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Hi!
I am about to start playing with the FlowCam and ZooPhytoImage, and would be also interested to get any new updated plugin if possible, as well as any advice you can provide.
Thanks!
Enric
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Hi,
I think the best thing is to send me an example dataset (acquire two or three collages), zip the sample directory and attach it here. That way I can be sure the plugin operates with your data.
Cheers,
Ben
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