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Hi All. I'd like to be able to load intensity cell/tissue images and a corresponding segmentation. Is it possible to load multiple files and stack them in this way? Or would you have to stack the channels (probably as a tif) and eventually load the single file. Thanks in advance for any thoughts or ideas. |
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Replies: 2 comments 10 replies
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Our vitessce framework is what you would use for that since the rendering for segmentation results is non-trivial - see vitessce.io for more information. You could do what you are describing in theory, I suppose. For example: https://portal.hubmapconsortium.org/browse/dataset/79ec9402362b276b9e12c0f596dbac4f If it is taking a bit to load, you can just x-out the heatmap. |
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Okay now I was able to stack channels in such a way that Viv displays the dimensions as 5/5 [1, 2, 1, 1166, 1053] which according to what I've seen previously would mean it would display 2 channels. For some reason the 2 is still being read as Z which create a slider with a single channel. There must be some specific piece of metadata that's telling Viv a dimension ordering?
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@lstrgar It's very hard to say what is going on here. Could you share data? |
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Appreciate the offer to take a look. I can definitely share the sample in question. Does box work okay? Even if you don't have an account I should be able to share with you if you provide an email address where Box can send an invitation. |
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That's fine, yes. |
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I think I resolved this issue. It doesn't appear to be a matter of dimension order. Rather you must explicitly tell bioformats which dimension you want to stack the files on. So far, the best option for this is using a pattern file -- https://docs.openmicroscopy.org/bio-formats/6.8.1/formats/pattern-file.html. I've had success using a pattern file as input to bfconvert but was told that it can also with with bioformats2raw and raw2ometiff For example, with two tiff single image channels (each HxW), c0.tiff and c1.tiff, you could populate a a file called stack.pattern with "c<0-1>.tiff" and then replace the input file in your bfconvert call with stack.pattern. |
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I think I resolved this issue. It doesn't appear to be a matter of dimension order. Rather you must explicitly tell bioformats which dimension you want to stack the files on. So far, the best option for this is using a pattern file -- https://docs.openmicroscopy.org/bio-formats/6.8.1/formats/pattern-file.html. I've had success using a pattern file as input to bfconvert but was told that it can also with with bioformats2raw and raw2ometiff For example, with two tiff single image channels (each HxW), c0.tiff and c1.tiff, you could populate a a file called stack.pattern with a single line that reads "c<0-1>.tiff" and then replace the input file in your bfconvert call with stack.pattern. |
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I think I resolved this issue. It doesn't appear to be a matter of dimension order. Rather you must explicitly tell bioformats which dimension you want to stack the files on. So far, the best option for this is using a pattern file -- https://docs.openmicroscopy.org/bio-formats/6.8.1/formats/pattern-file.html.
I've had success using a pattern file as input to bfconvert but was told that it can also with with bioformats2raw and raw2ometiff
For example, with two tiff single image channels (each HxW), c0.tiff and c1.tiff, you could populate a a file called stack.pattern with a single line that reads "c<0-1>.tiff" and then replace the input file in your bfconvert call with stack.pattern.