FLIM data analysis with FLIMJ

Hi @Xanthorapedia and @ctrueden,

First and foremost, thanks for your work on FLIMJ. I have been recently trying to use your plugin FLIMJ on my datasets, for instance the one here where the Channel 2 is of interest for lifetime info. The long lifetime can be fixed to 3.5 nsec.

There are issues that I have faced:

  1. The plugin requires an already opened SDT files to initiate. Since the data is loaded as Hyperstack with 256 or 512 time point, it takes a lot to open the data. Could that be implemented that while starting the plugin, a pop-up widow asks the user to choose the file to open?
    As an experience, this is already implemented in SLIMCurve and functions really fast

  2. To be able to run the plugin, I have to use a freshly downloaded Fiji. Although it work fine your dateset, the plugin returns the warnings quoted below while opening my 2-channel FLIM data. Can it be because the dateset includes TWO channels?

Sep 07, 2020 1:58:58 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172
Sep 07, 2020 1:58:59 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172
Sep 07, 2020 1:58:59 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172
Sep 07, 2020 1:58:59 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172
Sep 07, 2020 1:58:59 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172
Sep 07, 2020 1:58:59 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 11.0.1 by JavaFX runtime of version 8.0.172

  1. How is it possible to adjust the Brightness/Contract of intensity images in FLIMJ?
  2. On my PC, changes in “Kernel Size” OR “Bin all pixels” control does not function (I have waited up to 5 minutes so far) . What would be the reason?
    Please find a recording regarding some this issues in this video

Thanks and cheers,
Ali

2 Likes

Hi Ali @AGeisari,

Thanks for trying out our new plugin and providing detailed feedback. I did some investigation into your use case and regarding your concerns:

  1. Are you referring to the time when trying to open the dataset in Fiji or the time spent when launching the plugin? For the former, it is bound to ImageJ’s image IO service and there is nothing we can do on the plugin side to improve; I wouldn’t expect a pop-up to help as much because it will go through the same IO service unless we implement our own dataset parser. Another consideration is that the plugin is designed to be as source-ignorant as possible, meaning that it doesn’t make assumptions about whether the dataset is coming from a file on disk or from a preprocessing script in Fiji.
    If you are referring to the later, I just found a little catch: If you are opening with Bio-Formats, make sure you choose “View stack with: Hyperstack” instead of “Standard ImageJ”, which is deprecated:
    image
    Internally, it seems to take much less time to convert a dataset (PlanarImg) opened with the former option from UnsignedShortType to FloatType when populating metadata (@ctrueden any insight as to why?)
  2. The (admittedly annoying) warnings always show up regardless but are totally harmless. See reason in my comment here.
  3. It’s a nice setting to have, but unfortunately, there is no way to do that in the current version. A workaround would be to export the intensity image in the “Export” panel and adjust the brightness/contrast in Fiji.
  4. That was a known issue in an earlier version. It was caused by the binning failing due to e.g. incorrectly interpreted metadata (not the user’s fault), only that this kind of error was reported in the console (they are now for debug purposes).
    I remember fixing this problem, but the update site was out of sync with the repository. The issue should go away if you upgrade the plugin to the newest v1.1.0 in Fiji Updater. After that, you may need to manually replace the imagej-ops-0.45.2.jar with imagej-ops-0.45.5.jar in your Fiji.app/jars in order for binning to work properly. This is just an ad hoc workaround before Fiji’s imagej-ops version catches up.

Your dataset seems to be working on my machine with this new version:

Please let me know if that works for you as well.

As a side note, I am no longer an active developer of the FLIMJ project. For minor bug fixes and feature requests, you are welcome to fire github issues as a note to future developers or, better, submit pull requests. However, I will do my best to answer questions and help with investigating major problems.

All the best!

3 Likes

Hi @Xanthorapedia,

Thanks a lot for the response. It’s been helpful and solving the issue.
I have other topics to mention for instance about different file extensions which can be addressed under another topic.

Best wishes,
Ali