Extract TIFF images from a density map
Hi all,
I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map. Now I would like to extract all the planes in TIFF images. Is this possible? Could you suggest to me how to deal with it? Thank you for your kind attention. Have a great day,
Andrea
Hi Andrea,
ChimeraX does not have a command to write map data in TIFF format. But I could add that ability today. Do you want each plane of a map written to a separate TIFF file, or all planes written to one file, or do you just want to show one specific plane and write it out as TIFF? You know the TIFF format doesn't have the pixel size for your map unless it is written in using some specific extra info for example using an ImageJ TIFF header or OME TIFF header. What software do you intend to use these TIFF images in?
Tom
On Dec 15, 2020, at 4:19 AM, Andrea Dallapè andrea.dallape@unitn.it wrote:
Hi all,
I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map. Now I would like to extract all the planes in TIFF images. Is this possible? Could you suggest to me how to deal with it? Thank you for your kind attention. Have a great day,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom,
thank you for your prompt and kind reply. It would be amazing! My idea is to have each plane of the map in a separate TIFF file (ie 400 plane, 400 images). I didn’t know about the pixel size, but I will use ImageJ, so it seems to be perfect. Thank you for your help and efforts. Have a great day,
Andrea
Il giorno mar 15 dic 2020 alle 18:11 Tom Goddard goddard@sonic.net ha scritto:
Hi Andrea,
ChimeraX does not have a command to write map data in TIFF format. But I could add that ability today. Do you want each plane of a map written to a separate TIFF file, or all planes written to one file, or do you just want to show one specific plane and write it out as TIFF? You know the TIFF format doesn't have the pixel size for your map unless it is written in using some specific extra info for example using an ImageJ TIFF header or OME TIFF header. What software do you intend to use these TIFF images in?
TomOn Dec 15, 2020, at 4:19 AM, Andrea Dallapè andrea.dallape@unitn.it
wrote:
Hi all,
I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract
TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map.
Now I would like to extract all the planes in TIFF images. Is this
possible? Could you suggest to me how to deal with it?
Thank you for your kind attention. Have a great day,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Andrea,
I added saving of TIFF maps in ChimeraX, will be in tomorrow's ChimeraX builds.
https://www.rbvi.ucsf.edu/chimerax/download.html#daily https://www.rbvi.ucsf.edu/chimerax/download.html#daily
It saves a normal TIFF file but there is a tag (ImageDescription) used by ImageJ that has the pixel size, so I called the format "ImageJ TIFF map" in ChimeraX. By default it saves all z-planes in one file
save mymap.tif format imagejtiff
If you have more than one map open in ChimeraX you need to specify which one to save
save mymap.tif format imagejtiff model #1
If you want to save each z-plane as a separate file
save mymap_{z}.tif format imagejtiff
The {z} in the name will files mymap_000.tif, mymap_001.tif, ... where the {z} is replace by the plane number (starting at 0).
The "format imagejtiff" option is needed because without that it just saves a photo of the graphics window. Currently the Save dialog shown by menu File / Save... cannot save ImageJ TIFF because there are two types of files with suffix ".tif", graphics photos and ImageJ and we need to add some magic to the code that can handle that situation. That will be done later. But for now you have to use the command.
Another limitation of the ImageJ TIFF save is it only handle single channel data. In the future I could make it handle multichannel (e.g. light microscopy with red,green,blue channels) data.
Tom
On Dec 15, 2020, at 9:21 AM, Andrea Dallapè andrea.dallape@unitn.it wrote:
Hi Tom,
thank you for your prompt and kind reply. It would be amazing! My idea is to have each plane of the map in a separate TIFF file (ie 400 plane, 400 images). I didn’t know about the pixel size, but I will use ImageJ, so it seems to be perfect. Thank you for your help and efforts. Have a great day,
Andrea
Il giorno mar 15 dic 2020 alle 18:11 Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> ha scritto: Hi Andrea,
ChimeraX does not have a command to write map data in TIFF format. But I could add that ability today. Do you want each plane of a map written to a separate TIFF file, or all planes written to one file, or do you just want to show one specific plane and write it out as TIFF? You know the TIFF format doesn't have the pixel size for your map unless it is written in using some specific extra info for example using an ImageJ TIFF header or OME TIFF header. What software do you intend to use these TIFF images in?
TomOn Dec 15, 2020, at 4:19 AM, Andrea Dallapè <andrea.dallape@unitn.it mailto:andrea.dallape@unitn.it> wrote:
Hi all,
I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map. Now I would like to extract all the planes in TIFF images. Is this possible? Could you suggest to me how to deal with it? Thank you for your kind attention. Have a great day,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
The Save dialog will also save ImageJ TIFF in tomorrow's ChimeraX in addition to the save command.
Tom
On Dec 15, 2020, at 5:09 PM, Tom Goddard goddard@sonic.net wrote:
Hi Andrea,
I added saving of TIFF maps in ChimeraX, will be in tomorrow's ChimeraX builds.
https://www.rbvi.ucsf.edu/chimerax/download.html#daily https://www.rbvi.ucsf.edu/chimerax/download.html#daily
It saves a normal TIFF file but there is a tag (ImageDescription) used by ImageJ that has the pixel size, so I called the format "ImageJ TIFF map" in ChimeraX. By default it saves all z-planes in one file
save mymap.tif format imagejtiff
If you have more than one map open in ChimeraX you need to specify which one to save
save mymap.tif format imagejtiff model #1
If you want to save each z-plane as a separate file
save mymap_{z}.tif format imagejtiff
The {z} in the name will files mymap_000.tif, mymap_001.tif, ... where the {z} is replace by the plane number (starting at 0).
The "format imagejtiff" option is needed because without that it just saves a photo of the graphics window. Currently the Save dialog shown by menu File / Save... cannot save ImageJ TIFF because there are two types of files with suffix ".tif", graphics photos and ImageJ and we need to add some magic to the code that can handle that situation. That will be done later. But for now you have to use the command.
Another limitation of the ImageJ TIFF save is it only handle single channel data. In the future I could make it handle multichannel (e.g. light microscopy with red,green,blue channels) data.
Tom
On Dec 15, 2020, at 9:21 AM, Andrea Dallapè <andrea.dallape@unitn.it mailto:andrea.dallape@unitn.it> wrote:
Hi Tom,
thank you for your prompt and kind reply. It would be amazing! My idea is to have each plane of the map in a separate TIFF file (ie 400 plane, 400 images). I didn’t know about the pixel size, but I will use ImageJ, so it seems to be perfect. Thank you for your help and efforts. Have a great day,
Andrea
Il giorno mar 15 dic 2020 alle 18:11 Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> ha scritto: Hi Andrea,
ChimeraX does not have a command to write map data in TIFF format. But I could add that ability today. Do you want each plane of a map written to a separate TIFF file, or all planes written to one file, or do you just want to show one specific plane and write it out as TIFF? You know the TIFF format doesn't have the pixel size for your map unless it is written in using some specific extra info for example using an ImageJ TIFF header or OME TIFF header. What software do you intend to use these TIFF images in?
TomOn Dec 15, 2020, at 4:19 AM, Andrea Dallapè <andrea.dallape@unitn.it mailto:andrea.dallape@unitn.it> wrote:
Hi all,
I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map. Now I would like to extract all the planes in TIFF images. Is this possible? Could you suggest to me how to deal with it? Thank you for your kind attention. Have a great day,
Andrea _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Andrea Dallapè -
Tom Goddard