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superresolved.com • View topic - beginner questions about 3B

beginner questions about 3B

Bayesian analysis of blinking and bleaching

beginner questions about 3B

Postby oscar » Thu Feb 06, 2014 8:53 pm

I have just started to learn how to run 3b lately. Here are my questions.

I was following the example in the tutorial. The command is
./multispot5_headless --save_spots test_data/results.txt --log_ratios test_data/markup1.bmp test_data/test.tif

results.txt should be the output. However what does markup1.bmp do and how is it generated?

Also, I have access to a big cluster and would like to take advantage of the parallel capability. My understanding is threeB itself is not parallelized. I have to split the image and run 3b on each subarea and combine them at the end. Is there a simple way to split the image? And how do I combine the results after running multispots5_headless in "parallel"?

Thanks
oscar
 
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Joined: Thu Feb 06, 2014 7:28 pm

Re: beginner questions about 3B

Postby edrosten » Tue Feb 11, 2014 3:16 pm

edrosten
 
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Joined: Wed Jul 18, 2012 2:54 pm

Re: beginner questions about 3B

Postby oscar » Mon Feb 17, 2014 6:51 pm

Thanks, Ed, for the detailed instructions. I will give it a try. I have gimp installed. How do exactly I generate the markup file though? I can't seem to find the option from the menus.
oscar
 
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Joined: Thu Feb 06, 2014 7:28 pm

Re: beginner questions about 3B

Postby edrosten » Thu Feb 20, 2014 10:28 pm

Take a single frame or a z project of the data (this example is taken from the test data):

AVG_test_data.png
AVG_test_data.png (4.28 KiB) Viewed 37622 times


Load it into the GIMP:

image-1-basic.png
image-1-basic.png (22.78 KiB) Viewed 37622 times


Bring up the layer dialog and add a transparent layer in front of the image:

image-3-layer.png
image-3-layer.png (38.62 KiB) Viewed 37622 times


Set the colour to white, and select the pencil tool (not the brush) and set it to an appropriate size. Draw over the areas you wish to be analysed:

image-4-dot.png
image-4-dot.png (62.99 KiB) Viewed 37622 times


Now, select the back layer (the original image) and fill it with black:

image-5-fill.png
image-5-fill.png (30.65 KiB) Viewed 37622 times


Save the resulting file as a PNG by going to File>Export:

AVG_test_data2.png
AVG_test_data2.png (283 Bytes) Viewed 37622 times


If you use the final image as the markup, then the area under the white dot will be analysed.


This is generally the method I've used for creating markup.
edrosten
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

Re: beginner questions about 3B

Postby oscar » Mon Mar 17, 2014 9:15 pm

Hi Ed,
I followed your instruction to create markup files and got a better understanding of the process. Still have a few questions:

1. So the idea is to divide up the whole image into subareas. This way 3B analysis of subareas can be run at the same time in parallel. To do that, the smaller jobs still have to be initiated manually, Am I correct?

2. If there are a lot of tiff files to be processed, with the command "multispot5_headless --save_spots results-0000.txt --log_ratios markup_small_0000.png --dilate_mask_as_filter_radius 3.2
data/image-*.tiff", how are the files processed? Are the subareas of each frame being processed simultaneously? The next tiff image will be processed once all the subareas of first image is done processing? So if there are 100 60x60 images with markup size of 15x15, the program will generate 16x100=1600 result files?

3. My understanding is that, the image quality will be improved (signal noise ratio enhanced) after running 3B which will result in a new set of images with same dimensions as the inputs. Is that right?
oscar
 
Posts: 3
Joined: Thu Feb 06, 2014 7:28 pm

Re: beginner questions about 3B

Postby edrosten » Mon Mar 24, 2014 9:30 pm

edrosten
 
Posts: 42
Joined: Wed Jul 18, 2012 2:54 pm

Re: beginner questions about 3B

Postby hibaaryan » Tue Jan 06, 2015 4:47 pm

We're comparing the results imagej plugin and the results of the compiled program, we're using the same configurations on the mustilspot5.cfg but the results aren't the same, the later reconstruction seems to have less quality. The version of 3B is 1.1 in the two cases. Could you please advise us about it?

Another question, I'm just wondering if the 'iterations' shown the result file of imagej plugin are the same as the 'iterations' that are shown in the result file of the compiled program, i.e. does the algorithm needs to be stopped by the "Iteration: 50(200)"?
hibaaryan
 
Posts: 1
Joined: Tue Jan 06, 2015 4:34 pm

Re: beginner questions about 3B

Postby hoha » Fri Jan 09, 2015 3:10 am

Hi hibaaryan,

I did this questions some time ago and ed and susan had replied , I didn't understand what are u looking for?

Rewards,
Haydee.
hoha
 
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Joined: Mon Apr 14, 2014 9:24 pm


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