Colocalization imagej software
* What exactly is insufficient about the Coloc 2 plugin * What exactly you are trying to accomplish As such, it is important for users to be patient when reporting issues see this FAQ entry for details:
Colocalization imagej software software#
The ImageJ community supports the software largely on a volunteer basis, as time and energy permits. Please understand that ImageJ and Fiji are open source software projects, not commercial software products. > little intention of completing the work apparently. > plugin is effectively half finished and the writer of the plugin has > colocalisation analysis for their scientific research. > This is a major issue for those in the community who need He is also an asset to the community and as you can see from his GitHub profile ( ), he is still very active in development of related software projects. If you refer to Tom Kazimiers, the main developer: AFAIK he currently works at HHMI Janelia Research Campus, as part of Albert Cardona's group. Dan is one of the most talented, friendly and helpful members of the community with whom I have had the pleasure of working. If you refer to Dan White, the project lead: he is still active in the community and tries to help with Coloc 2 issues when he has time (e.g., just today: ). > MPI in Dresden and are now working for a company. > I have now discovered that the person who was writing and supporting It would be much better to discuss these social issues on the ImageJ mailing list. However, please note that this is an issue tracker, not a general discussion forum. Thank you for continuing to engage the ImageJ community in this discussion! Manager of Edinburgh Super-resolution Consortium IGMM. Head of Advanced Imaging Resource, IGMM, University of Edinburgh. I don't program Java and have no time to learn so can't offer to help personally, I have discussed this at ELMI with the bioimage community so I am aware its a known issue. I can see if my image informaticist might be interested as a last recourse. But what would happen in this circumstance, when the person tasked with reimplementing the plugin gives up half way through? Clearly the job needs to be completed. Likely the MPI-Dresden will be taken up coding plugins for SPIM, such as Big data viewer and presumably wouldn't have personnel to finish the project.Ĭolocalisation was reliably and robustly implemented in IJ1 and needs must IJ2 / FIJI should at least be able to reproduce the functionality available in IJ1 in newer versions. In fact they tried to sell me their companies products in response to my query about Coloc2. Since the plugin is effectively half finished and the writer of the plugin has little intention of completing the work apparently. This is a major issue for those in the community who need colocalisation analysis for their scientific research. This explains why the plugin has been broken for such a long time. They have apparently left the MPI in Dresden and are now working for a company. Run("Colocalization Finder.I have now discovered that the person who was writing and supporting Coloc2 in Fiji is no longer doing so.
![colocalization imagej software colocalization imagej software](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41598-017-02735-8/MediaObjects/41598_2017_2735_Fig1_HTML.jpg)
Where you can additionally define the position of the analysis ROI within the scatter plot (this feature was needed by a colleague)."
Colocalization imagej software download#
"I made a "more advanced" version of the plugin that you can download under the following link:
![colocalization imagej software colocalization imagej software](https://d3i71xaburhd42.cloudfront.net/cf4d9f08ded63eddb8fee9aed8e9487b2e7a7478/3-Figure2-1.png)
However, personal communication from the author: However, statistics are not reported for this type of ROI.Ī problem is that when drawing the ROIs, the exact value for setting a threshold is not shown.The XY location is shown, but this is the pixel location, not the intensity value. Using the shift key to add a first point for the second ROI and then releasing it, followed by completion of the ROI, the pixels that are not correlated are highlighted. On the scatterplot, drawing a rectangle or overlapping reactangles (use Shift key) or an oval or overlapping ovals (use Shift key)and then clicking in the ROI results in a reporting of statistics for this region. Analysis can be restricted to pixels having values with a minimum ratio." Drawing a rectangular selection on this diagram allows you to highlight corresponding pixels on a RGB overlap of the original images, and if selected, on a 3rd image. Is an excellent interactive tool for looking at colocalization.ĭescription from the original webpage: "This plugin displays a correlation diagram for two images (8bits, same size).