search

abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
Other
78 stars 32 forks source link

Stitching 4+ channels together #39

Open pawlowac opened 5 years ago

pawlowac commented 5 years ago

Hi,

What is the simplest way to stitch an image together with 4+ channels? I plan to stitch up to 30 images each with 4+ channels, and I'm hoping to streamline it as much as possible.

I appreciate your assistance and advice!

Thanks, Andrew

iannellog commented 5 years ago

I can try to guide you, but consider that I am very busy in next days, so I could not be able to interact quickly. However I first need to understand how channels are acquired and stored. Please answer as much precisely as possible to the following questions:

-- Giulio

Il giorno mar 23 ott 2018 alle ore 18:57 pawlowac notifications@github.com ha scritto:

Hi,

What is the simplest way to stitch an image together with 4+ channels? I plan to stitch up to 30 images each with 4+ channels, and I'm hoping to streamline it as much as possible.

I appreciate your assistance and advice!

Thanks, Andrew

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/39, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1utZfh0fFP_4dhqqs_NnDx71DGlNks5un0pogaJpZM4X2CUm .

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

pawlowac commented 5 years ago

HI Dr. Iannello,

Thank you for your assistance.

  • are channels of each tile stored in the same files or each channel is stored in a different file (in the formar case which format are you using since your images may have more than 3 channels)?

Ideally we'd like to have all channels in the same file, but we are flexible. We are exporting tif files from Nikon elements and we have the option of all channels in the same tif, RGB, or one tif per channel. I'm thinking I need to generate the xml_merging.xml file for one channel, then using that xml_merging.xml file to stitch the other channels. (e.g., complete stitching for channel 3, then use the channel 3 xml_merging.xml file to merge channel 1, 2, and 4).

  • in case channels are stored in different files, the tile matrices corresponding to different channels have the same structure?

Yes, the x-y-z coordinates are the same for each channel.

  • in case channels are stored in different files, the folders corresponding to different channels are subfolders of a common folder or there is a different root directory for each channel?

I haven't attempted this and I am wondering what your advice would be. I have only stitched one channel so far. Ideally it would be (I think) a 3-level hierarchical folder (i.e., '/channel_1/FFFFFF/FFFFFF_SSSSSS/FFFFFF_SSSSSS_ZZZZZZ.tif') but I am open to your advice.

  • how do you perform the import of a single channel image: do you configure your tiles according to the two-level hierarchy of folders and use the import step of TeraStitcher to generate the xml_import.xml file or, alternatively, you generate the xml_import.xml file with an independent tool without performing the import step of TeraStitcher?

Currently I generate the xml_import.xml file using the --import command with the two-level hierarchy folders (i.e., /FFFFFF/FFFFFF_SSSSSS/FFFFFF_SSSSSS_ZZZZZZ.tif')

Best, Andrew

iannellog commented 5 years ago

Just one more question. Are you using the GUI version of TeraStitcher or the command line one? You can perform multi-channel stitching in both cases, but the procedure is slightly different

Giulio

Il mer 24 ott 2018, 15:56 pawlowac notifications@github.com ha scritto:

HI Dr. Iannello,

Thank you for your assistance.

  • are channels of each tile stored in the same files or each channel is stored in a different file (in the formar case which format are you using since your images may have more than 3 channels)? Ideally we'd like to have all channels in the same file, but we are flexible. We are exporting tif files from Nikon elements and we have the option of all channels in the same tif, RGB, or one tif per channel. I'm thinking I need to generate the xml_merging.xml file for one channel, then using that xml_merging.xml file to stitch the other channels. (e.g., complete stitching for channel 3, then use the channel 3 xml_merging.xml file to merge channel 1, 2, and 4).

  • in case channels are stored in different files, the tile matrices corresponding to different channels have the same structure? Yes, the x-y-z coordinates are the same for each channel.

  • in case channels are stored in different files, the folders corresponding to different channels are subfolders of a common folder or there is a different root directory for each channel? I haven't attempted this and I am wondering what your advice would be. I have only stitched one channel so far. Ideally it would be (I think) a 3-level hierarchical folder (i.e., '/channel_1/FFFFFF/FFFFFF_SSSSSS/FFFFFF_SSSSSS_ZZZZZZ.tif') but I am open to your advice.

  • how do you perform the import of a single channel image: do you configure your tiles according to the two-level hierarchy of folders and use the import step of TeraStitcher to generate the xml_import.xml file or, alternatively, you generate the xml_import.xml file with an independent tool without performing the import step of TeraStitcher? Currently I generate the xml_import.xml file using the --import command with the two-level hierarchy folders (i.e., /FFFFFF/FFFFFF_SSSSSS/FFFFFF_SSSSSS_ZZZZZZ.tif')

Best, Andrew

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/39#issuecomment-432667365, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1qiq_9WxNSDK7NNtioc1BjAEpUIdks5uoHGLgaJpZM4X2CUm .

pawlowac commented 5 years ago

I'm using the command line version.

Andrew

iannellog commented 5 years ago

Andrew, I have prepared a demo for multi-channel stitching, but I need your direct email to send you attachments.

-- Giulio

Il giorno mer 24 ott 2018 alle ore 22:18 Andrew Pawlowski < notifications@github.com> ha scritto:

I'm using the command line version.

Andrew

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/39#issuecomment-432812790, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1tMY08yzZ5NMHs7Z80M6g1sCCje-ks5uoMsggaJpZM4X2CUm .

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

pawlowac commented 5 years ago

Fantastic, thank you!

My email is andrew_pawlowski at hms dot harvard dot edu

Andrew

JeffreyStirman commented 4 years ago

Would I also be able to get this demo? I too need to stitch 3-4 channels of images and curr use the folder structure mentioned above: /channel_1/FFFFFF/FFFFFF_SSSSSS/ZZZZZZ.tif

iannellog commented 4 years ago

Sorry for the delay of the answer, but I am in vacations until the end of Augurst.

Attached you will find:

Make reference to the TeraTools Guide accessible from the GitHub site; it is not always easy to read, but may perhaps help you in better understanding the procedure described in the README file; look at section 1.8 and Appendix C for details about multi-channel stitching.

Let me know if you get to save the attachment.

I hope this may help.

-- Giulio

multi-channel-stitching-demo.zip