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JACoP BIOP Version
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Oli implemented a few extra features to JACoP via a refactoring of the original JACoP code.

The repository is hosted on C4Science at rJACOPB.

Plugins › BIOP › Image Analysis › BIOP JACoP

Based on JACoP

Available methods/metrics

Pearson correlation coefficient
Mander's coefficient article
Costes article
Li article

Input

  • A multi-channel image ( no need to split into independent channels)
  • Define channels to use
  • Define Threshold, either using an Automatic Thresholding Method or a User manually fixed value.


We recommend to use Automatic method. It will compensate for subtle changes in illumination (microscopes are not perfect), or in case of variable expression of Fluorescent Proteins, the intensity from one cell to another (it woul need ROIs that define each cell).
Nevertheless, it might fail if your images are very heterogenous (number of cells, intensities range, areas of signal...)
If you can't find any method that gives satisfying result, consider then using a fixed value, manually set.

We urge you to have controls (mono stained samples, acquired the same way as the test ones, same number of channels ...) to verify that the defined thresholds are above the signal one can observe in an unstained sample. You will always have some crosstalk/bleedthrough, always!

Output

  • Results Table
  • Output Image with Thresholded Mask, FLuorogram (optionnal), Random image (new feature in BIOP JACoP)

Some Functionnnalities

Region of Interest (ROIs)

With many ROIs in the ROI manager (defining cells for exemple), you will get an analysis per ROI.

  • Crop ROIs , generates a cropped iamge for each ROI.

Z-stack

  • Consider Z slices Separately , output a single Z-stack image BUT the analysis are performed on each individual slice.

We recommend starting your pilot experiment , with z-stack and asses if the result depends of doing the analysis on 2D or 3D image and continue your acquisition campaign accordingly

  • Set Auto Thresholds On Stack Histogram , when using one of the Automatic Thresholding Method you can use the method on individual slice or on the entire stack.

Set Advanced Parameters

to set size of the fluorogram

Install

Please use PTBIOP update site

Macro

Macro using this tool to manage a folder and remember parameters, using BIOP BASICs

macro_JACOPb_BIOPBasics.ijm4 KBDownload

Last Author
romainGuiet
Last Edited
Feb 13 2020, 10:33

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