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test annotation data download #20
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At the bottom of that webpage, look for
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thanks @vzickus I downloaded that, but it is for full brain not for half brain. |
@vzickus if you are using |
Ah, you can just split it yourself (e.g. using ImageJ or otherwise). |
@crazyhottommy I'm afraid I can't say I have done it successfully! It would be interesting to compare notes if you ever get round to validating the cell counting (localization accuracy of humans vs machine). |
Happy to share my notes. it is here https://hackmd.io/IKmM1BeVSyG4LDf_Q1dG0Q?view BTW, the elastix version matters or not? I got this
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4.9 worked fine for me. It's been a while since I used the whole thing, so don't remember the output (but it does not seem to be crashing?). I am mostly focusing on optimizing cell counting at the moment. I feel there might be some bugs left in the code (I tried following the tutorial from the supplementary materials from their 2016 paper, but couldn't complete it because of some issue that I did not yet manage to track down). Although my "debugging" is inserting |
It is not crashing, just no images were processed
hmm...so this package is not maintained anymore by the author? but if there are enough interests, we can do together to revive this library? |
@vzickus BTW this is Ming Tang, I am working for Catherin Dulac lab on some imaging data. Nice to meet you. I can be reached at tangming2005ATgmail.com |
Actually, I seem to recall something like that. If you test elastix by itself from terminal, it should work no problem. I think the issue was with paths. EDIT: Actually, I had raised an issue about something similar, check the closed #12 issue. |
Thanks, Ming. I've e-mailed you to avoid spamming here. |
I had something similar to #12 before, and it seems the folder name has space (the folder was downloaded from the link you gave), I later removed the space and it worked. I guess this error is the same here because the image tif files(downloaded from osf) have spaces as well. |
Can either off you provide some help on how to split the annotation file in Image J? Feel free to contact me at Antonio.aubry@mssm.edu. Thanks! |
@aaubry89 I think you want the function "Stack splitter". |
Thanks, do I also need to split the .nrrd annotation file or just the .tif annotation file? |
Hi Chris,
Where can I download the annotation files for your test data(half brain tif)?
I only found the full brain tif from https://idisco.info/clearmap-2/
Thanks!
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