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macronucleus / Chromagnon

Image correction software for chromatic shifts in fluorescence microscopic images
GNU General Public License v2.0
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Unable to open 2D t-series images #17

Closed biophyschem closed 5 years ago

biophyschem commented 5 years ago

Hi, I'm trying to import 2D t-series tif images with two colors as 16-bit composite files, but no files were appeared on the list. As an example, Chromagnon can import images with 20 slices of c=2, t=1, z=10 but cannot open those with 20 slices of c=2, t=10, z=1. How can I open the former ones? Thanks.

macronucleus commented 5 years ago

It is likely that Chromagnon cannot read your file format, since a 2D t-series tif image worked fine for me. Are you be willing to share your tif file with me? I will put a link to upload your file here tomorrow. Thanks.

macronucleus commented 5 years ago

I am sorry, it will be on the next Monday to put a link here. I could not connect to our server remotely today.

biophyschem commented 5 years ago

That's just fine with me. Thanks!

macronucleus commented 5 years ago

Here is the link to upload your tif file. https://fexcc.nict.go.jp/user/~tg/gnt7n9oaajd47ig8rg53s72oc4 password: vq6Y57kkr4

By the way, are you using source installation of Chromagnon (v 6.9)? If so, then the inability to read the time series is due to a different reason (I have mistakenly disabled to input image files with a single wavelength; I have fixed in my computer but not on GitHub yet).

biophyschem commented 5 years ago

I failed to log in to the system since log-in ID as well as password must be filled in the log-in window. So I have uploaded a sample image file here. I acquired the image with two different cameras, and made the composite file with Fiji. I installed the Windows edition of the software on GitHub (Chromagnon065Win.zip).

TestImage.zip

macronucleus commented 5 years ago

I am sorry for putting a wrong link, and thank you for uploading your file in a public place. I have located the problem in my code and already fixed in my computer. I will make sure everything works before releasing the next version, since I have also made a lot of changes in the next release. I believe you can use the new version by the end of the next week. Please be patient.

biophyschem commented 5 years ago

Thanks a lot! I'm looking forward to the revision.

macronucleus commented 5 years ago

Hi, I have uploaded the new version v0.70. Please check the "release" tab. I believe the problem reading your tif file should be fixed.

By the way, with this version, you can choose wether to align the time axis or channels for a "multicolor timeseries image" from extra parameters dialog when you input such a file in the reference list.

biophyschem commented 5 years ago

Hi. This version works fine! Thank you very much for the quick response.