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LOADING .TIF FILES TO FIJI (DATASETS FROM CELLTRACKINGCHALLENGE)

Image Analysis
imagejfijicelltracking

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Nov 2021
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Nov 2021

Nov 2021

Anil AslihakAAslihak00
Nov 2021


As I am trying to form a dataset to train a model, I have to load the
preprocessed images to Fiji to create the dataset via the MiNTiF plug-in. So
far, I have loaded only .ims files which worked out pretty well mostly. To get
more experienced, I have downloaded datasets from celltrackingchallenge.net 6 .
It seems that all images in the datasets contain .tif files. So, I select all
the images, and then drag and drop to Fiji. Fiji successfully opens them but
opens each image in a different window. That’s impractical because if I’m not
going to close Fiji after the operation, I have to close each window one by one.
By the way, each image is a part of the same video sequence. So, I’d rather like
Fiji to open them in one window as a sequence of images, but I don’t know how.

Another problem is, in all the datasets from celltrackingchallenge.net 6 there
is only one channel. Is that because I might not be loading them to Fiji
properly? Theoretically, it might be the case that there is only one channel
(which is greyscale), but for microscopy images there are generally markers and
labels which correspond to different channels as far as I know. I am still going
to mail to ‘celltrackingchallenge’ as well, however; I thought bringing the
topic to the forum might be beneficial.





502 views 1 link


MicroscopyRAResearch_Associate
Nov 2021


From the descriptions and data types, it looks like there should only be one
channel, the channel that you are tracking. In other data sets you may indeed
have multiple channels, but once you start tracking, you will usually be
extracting the one useful channel anyway.

Generally piles of images are imported using Import image sequence, I think.
Though I haven’t done it much myself. Have you tried that?

1


11 days later
Anil AslihakAAslihak00
Nov 2021


No, I had not tried ‘import image sequence’. Fiji opened all the images in one
window that way, thank you!

1





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