"input must be an image stack not a single image" error

[gyu-ho-choi]

I expect this tool was extremely beneficial for my research

But i can't use this plugin because "input must be an image stack not a single image" message appears

• i installed BaSiC via Fiji updater

• i use fiji 64X version

• BaSiC is up to date (checked by Fiji updater)

• image file is Time series stack

• i upload screenshot about this problem
  
  
  

how can i fix it ?

Thanks

[tying84]

This is weird, maybe your time series has a different settings that BaSiC plugin recognise it as a single image. Could you try to save your timeseries as single images (one image per frame), and then import it into Fiji again? Best, Tingying

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On Mon, 4 Nov 2024 at 07:03, gyu-ho-choi ***@***.***> wrote: I expect this tool was extremely beneficial for my research But i can't use this plugin because "input must be an image stack not a single image" message appears - i installed BaSiC via Fiji updater - i use fiji 64X version - BaSiC is up to date (checked by Fiji updater) - image file is Time series stack - i upload screenshot about this problem Step1.png (view on web) <https://github.com/user-attachments/assets/8b543c72-2131-4200-9184-c23b2e5b58a6> Step2.png (view on web) <https://github.com/user-attachments/assets/cc0290f8-d069-4adf-932d-8bf009f79962> Step3.png (view on web) <https://github.com/user-attachments/assets/9ec5c711-b1c3-480c-9f42-15a53367197a> how can i fix it ? Thanks — Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACXOKO56NAPWPY4GPY2BY4LZ64E3BAVCNFSM6AAAAABRDRLELCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGYZTCOJSGIZDSNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[gyu-ho-choi]

Thanks for your reply

That image was acquired by Zeiss microscope, so original format was .CZI

Tried BaSiC process which i asked first issue was as follows
import CZI -> "duplicate" single channel with full Time series (yellow) -> "Save as" tiff -> BaSiC

So Technically, i tried BiSiC using single channel image.
i think "c:2/4" on top left derived from original file.
But that doesn't mean it's multichannel.

If there is another way to create "single images (one image per frame)", can you let me know?

i think some peoples have same problem
https://forum.image.sc/t/correcting-background-signal-in-time-lapse-imaging/26611#:~:text=Thanks%20for%20the%20suggestion.%20But%20as%20usual%20all%20these%20marvellous%20tools%20never%20work.%20I%20open%20my%20stack%20I%20run%20the%20Basic%20tool%20and%20complains%20saying%20my%20stack%20is%20not%20a%20stack%20is%20a%20single%20image.%20When%20it%20is%20clear%20is%20a%20stack%20of%20352%20frames.

i hope this plugin use widely by bug fixing

---

Additionally, do you think it is proper to use BiSiC process for FRET ratio images? (For example. Channel 1 intensity / Channel 2 intensity)

thanks

[tying84]

Okay, I guess that would be difficult as we do not maintain BaSiC anymore ( at least not now). Could you try BaSiCPy, the python based implementation gyu-ho-choi ***@***.***> schrieb am Mo. 4. Nov. 2024 um 12:51:

…

Thanks for your reply That image was acquired by Zeiss microscope, so original format was .CZI Tried BaSiC process which i asked first issue was as follows import CZI -> "duplicate" single channel with full Time series (yellow) -> "Save as" tiff -> BaSiC So Technically, i tried BiSiC using single channel image. i think "c:2/4" on top left derived from original file. But that doesn't mean it's multichannel. If there is another way to create "single images (one image per frame)", can you let me know? i think some peoples have same problem https://forum.image.sc/t/correcting-background-signal-in-time-lapse-imaging/26611#:~:text=Thanks%20for%20the%20suggestion.%20But%20as%20usual%20all%20these%20marvellous%20tools%20never%20work.%20I%20open%20my%20stack%20I%20run%20the%20Basic%20tool%20and%20complains%20saying%20my%20stack%20is%20not%20a%20stack%20is%20a%20single%20image.%20When%20it%20is%20clear%20is%20a%20stack%20of%20352%20frames . i hope this plugin use widely by bug fixing ------------------------------ Additionally, do you think it is proper to use BiSiC process for FRET ratio images? (For example. Channel 1 intensity / Channel 2 intensity) thanks — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACXOKOYJBEA6H3HVUROSSOLZ65NT5AVCNFSM6AAAAABRDRLELCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJUGUYTAMJYGU> . You are receiving this because you commented.Message ID: ***@***.***>

[gyu-ho-choi]

I've never used Python before
it will be difficult for me.....

Anyway thanks for your comment
If you come up with some solution, please let me know :)

[emmenlau]

Dear @gyu-ho-choi I think your problem can be solved with the help of ImageJ and/or Fiji alone. There is something in the way how you loaded and/or converted the CZI that makes the BaSiC plugin fail. I think you can get more help about this in the ImageJ and Fiji forums. This should not be too hard to achieve for a person knowledgeable with Fiji.

If you ask in the forums there, can you link it from here, so we can update the solution?

[gyu-ho-choi]

@emmenlau thanks your advice
i posted at Fiji forum
https://forum.image.sc/t/fiji-plugin-basic-input-must-be-an-image-stack-not-a-single-image-error/104574