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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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issues reading wavelength from TIF #23

Open DeboraOlivier opened 4 years ago

DeboraOlivier commented 4 years ago

image Hello,

I have separate reference images for the color pairs

To try do this, I saved a target file (original 4 channels) into 2 channels only in fiji using channel tools >split channels> merge relevant channels>save as tif. when I put it into chromagnon, the program doesn't recognize the wavelength information and doesnt run.

How can I force the program or tell it the identity of the wavelengths? Is there a way to edit this information? Is it possible to use different reference files to generate a single correction file (and then apply to 4-channel images)? Thanks in advance

Debora

macronucleus commented 4 years ago

Good question! I think the ImageJ file format does not contain wavelength information.

Splitting channels using software provided by the microscope company should keep the wavelength information.

If you need to use ImageJ, then at this moment, what you can do is first measuring chromatic shifts in the reference image by Chromagnon to make a “chromagnon.csv” file. Then you have to manually edit “.chromagnon.csv” file using a spread sheet program or on Chromagon viewer. The values in the column “wavelength” should be changed to 0, 1 in the order of channels in the image file.

Sorry for a clumsy solution. I will consider a smarter solution to edit wavelengths and combine multiple reference files.

DeboraOlivier commented 3 years ago

hi,following up on this (better late than never). I have modified the CSV so taht the wavelengths name fit that of the SIR.dv file. however, when I drag and drop in chromagnon v086, it doesn't work. What am I doing wrong? I acquire teh DAPI signal in the channels 527 / 603 and 679 (and sometimes also in 403). Reconstruct with Softworx then try to align Any help will be appreciated chromagnon_git.zip

macronucleus commented 3 years ago

Thank you for coming back to this issue. The chromagnon file seems okay to me. What does it happen if you try to align the target file with this file?

DeboraOlivier commented 3 years ago

Hi no the issue is that I can't drag/drop or open the CSV reference file via "References file" at all...DAPI_SIR_488-560-640.tif.chromagnon.csv I have Chromagnon v0.86 on windows 10 I have no clue why it doesnt like the csv - am trying to add java just in case

On Tue, Feb 16, 2021 at 2:35 AM macronucleus notifications@github.com wrote:

Thank you for coming back to this issue. The chromagnon file seems okay to me. What does it happen if you try to align the target file with this file?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/macronucleus/Chromagnon/issues/23#issuecomment-779527441, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSMXXLIWDDTOY3YBQFWDDDS7HDXRANCNFSM4IUI5FCQ .

DeboraOlivier commented 3 years ago

update: even after Java JDK install, I can't open the csv file...

macronucleus commented 3 years ago

That's right, there are dialects in the csv format (including Microsoft Excel). Please use Chromagnon v0.87 that I just uploaded in the release. Thank you.

DeboraOlivier commented 3 years ago

it seems to work now! cool! thanks

On Wed, Feb 17, 2021 at 3:50 AM macronucleus notifications@github.com wrote:

That's right, there are dialects in the csv format (including Microsoft Excel). Please use Chromagnon v0.87 that I just uploaded in the release. Thank you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/macronucleus/Chromagnon/issues/23#issuecomment-780260315, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSMXXI37ESV5YGMIUBHKVLS7MVFVANCNFSM4IUI5FCQ .