Hello,
I wish to register a time series of mitotic spindle images and found that the rigid registration is icy is suitable. The issue is that the registration runs on denoised images and I would like to apply the same transform on the raw images. Does anyone tried that on that plugin ?
Additional question: does anyone know where to find the source code of icy plugins and this one in particular. I found pieces of icy on GitHub but no plugin.
Many thanks for your help
Best
Jacques
Dear Jacques,
I am not sure to understand your question regarding denoised/raw images. I don’t see any information in the documentation of the Rigid Registration plugin restricting its use to denoised images. Or maybe, do you mean that you would like to do the registration on denoised images, get the transformation matrix and then use the transformation matrix to register the raw images?
The Rigid Registration plugin was developped by the Bioimage Analysis unit at the Institut Pasteur. The source code of plugins contributed by the BIA unit are publicly stored on the GitLab server of the Pasteur institute, in the BIA group: Bioimage Analysis · GitLab
Direct link to source code of Rigid Registration plugin: Bioimage Analysis / Rigid Registration · GitLab.
There is no common repository for plugins contributed by developers outside the BIA unit. We encourage developers to indicate location source code when filling the documentation of their plugins (see this blog post on how to publish a plugin on the Icy website).
Here I did it for the Rigid Registration plugin.
Best regards,
Marion
Dear Marion,
Thank you for your answer. Indeed I wish to do the registration on the denoised images and use the transform matrix on the raw images (your second alternative).
This is the first time I go under the surface for icy, but I am used to for other image processing softs (Matlab, Fiji,…). So let’s see if I manage.
Best
Jacques
Hello,
here is the modified jar to apply the registration (temporal / Simple mode) to a second sequence, in case it can help anyone. I also implemented a block to perform the same in protocols. I am not familiar to the icy deployment so I barely replace the original jar in icy plugin subfolder by mine :-). I can also push the edits to the gitlab (Who to ask to be permitted to do it if so?)
Best
Jacques
rigid-registration-1.3.2.jar (18.9 KB) ).
Dear Jacques,
Thank you for posting your modifications!
To push the edits to GitLab, you need to create a merge request on the GitLab repository of the Rigid Registration plugin, ie clone the project on your computer, create a branch, make your changes in this branch and push the branch on GitLab. We will then review the changes and merge them with the source code. Then, we will upload the new .jar on the Icy website and the new version of the plugin will be available for all in Icy.
In theory, anyone should be able to propose a merge request on the public repositories of BIA. If this is not the case, please contact @Stephane.
Don’t hesitate if you have questions.
Best regards,
Marion
