Correcting brightfield illumination artifacts

imagej

#21
  • I found the command using the search function, but the menu path does not show these entries.
  • running the plugin works for me on first try! :slight_smile:

Is it correct that the current input is one image file?


#22

Since it’s an ImageJ2 command, the Restoration submenu will turn up at the very bottom of the Plugins menu (see this issue).

Yes, it’s defined here:

Since you already used the search bar apparently, you should also see the Batch button that allows to process multiple files:

Right?


#23

got it! the scroll-down button was hidden due to my screen settings

also correct, and pretty awesome :slight_smile:
If I understand it correctly, then this allows me to repeat running the shading correction on as many images as I specify one-by-one.

I though a user might alternatively want to specify all images that should be considered in one “global” shading model, e.g. all single channel images from a plate, as the microscopes often save single images in this context.
They could of course be grouped manually/via script beforehand


#24

I’m not sure I understand what you mean. When running with Batch, you can choose any number of files (from a whole folder via the button, or simply dragged into the list fied). You choose which parameter will be “batched” (e.g. inputFile), and all other parameters will only be defined once for the whole batch. That means: a single shading model is used for all files in a given batch.

For more elaborate tasks such as “pairwise” batches of files each with an associated parameter set, I’d recommend using a tool that is more suitable for batch processing: #knime :slight_smile:

If your plugin is a well-defined SciJava Command annotated with headless=true, you’ll get an auto-generated KNIME node for free! So there not much keeping you from transitioning easily from the more interactive ImageJ to the more automated KNIME way of doing things…


#25

I think the point is about computing the shading model.
Currently, the plugin computes the shading model from “all images within each file”.
That means, one file could contain a tif stack and then the shading model would be computed based on all images in that stack (at least that is my understanding: https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html)
So currently, you would have to put all images that have the same shading into one big Tiff stack.
The output will be again one big Tiff stack, with all images corrected.
Would that work for you?


#26

yes that is what I was trying to say, thanks for clarifying :slight_smile:

yes that would work for me, that’s what I ment by: “they could be grouped beforehand”

Thanks again for the batch-able BaSiC, its really nice!