Debleach on a 3d stack timelapse

Hello all,

I have a 3d stack image over time. There is considering bleaching over the 40 minutes imaging I did. The debleach plugin seems to do the trick quite well except that it works in only one plane.
I couldn’t find a way to apply debleach to all the planes in the stack. I suspect there must be a way to do it with the protocols tool but I couldn’t find any documentation on it.

Does anyone have a suggestion on how to approach this?

Best, Jose.

Dear Jose,

Indeed, there might be a workaround with the protocols, but I can’t find an obvious one :frowning:
Let’s invite the developer of the Debleach plugin Thibault Lagache @lagache to join the discussion. Thibault, is there a way to apply the Debleach plugin on a 3D timelapse?

Best regards,
Marion

Hello Marion!!! Thanks a lot for the feedback!!
I have made some progress and I think I’m only one step away from actually making it.
I have used a slice loop from icy to pass each slice (and corresponding T frames) to the debleach plugin. This works as expected. The problem I have is that I get each slice separated from the rest.
I can manually Z merge this output but I have to do it manually and this is terribly time consuming and error-prone. I can’t find a way to Zmerge these slices withing protocols. Any suggestion?

Best and thanks again, jose.!

SampleZT-8bit.tif (15.0 MB)

BatchDeBleach.protocol (2.1 KB)

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Hi Jose,
Sorry for the late answer. Indeed, the Debleach plugin is only working with 2d sequences (for now…). I think you might be able to merge your 2d slices in a 3d stack by using a javascript block but I am not a real expert in javascript…like @Stephane :wink:
Let me know if you’re stuck, I might find some time to make the debleach plugin work in 3d
Thanks
Thibault

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Dear @boina

Here’s a protocol allowing you to re-stack the result in 3D :slight_smile:

BatchDeBleach3D.protocol (7.8 KB)

The only inconvenient is that Debleach block force to the intermediate slice so you need to close it.
@lagache It would be nice that when used in protocol mode, the Debleach plugin doesn’t show up the resulting sequence as we can freely manipulate it over the protocol (and show it up if needed).

Best,

– Stephane

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Thanks a lot @lagache and @Stephane!!! Lagache’s protocol works OK!!! The only problem I still have is I run out of RAM memory during the run but obviously that is not an icy issue!!

I thank again all the icy/bioimaging community for you feedback!!
Have a great day!!
Jose.

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Did you try to enable the virtual mode ? It can help when you run out of memory, that make the process (much) slower though (ans some plugins aren’t compatible with it)…

– Stephane

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Thank you @Stephane and @lagache for joining the discussion, and thank you @boina for testing Stéphane’s protocol!

To clarify Stéphane’s suggestion, the virtual mode is in the lower right corner of the ICY GUI, you can enable/disable it by clicking on the pile of disks.

Virtualmode2
Virtualmode

Another suggestion: check the amount of memory dedicated to Icy in the preferences, in the Max memory. The preferences menu is located in the upper left corner of the ICY GUI. I would allow Icy to use between 50% and 75% of the RAM. The value in the parentheses indicates the size of the RAM of your computer (here mine has 16Go of RAM and I allow Icy to use ~10Go max).

Preferences_button

Best regards,
Marion

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