What is the best tool in Debian to display Illumina sequencer's focus images ?
Hello everybody,
this time, I am asking a user question :)
I am inspecting raw image files from a sequencing run on the MiSeq platform
(Illumina), from the directory Images/Focus/L001/C1.1 that stores the images
related to focusing the instrument on the flow cell.
These images are in gray scale TIFF format of a depth higher than 8 bits. As a
consequence, tools such as Gimp or imagemagick ('display' command) show the
image completely black. Fortunately, ImageJ (many thanks to Andreas and
everybody for your work on it !) displays correctly the images. However, the
user interface of ImageJ is a bit unfriendly for naive users.
Here is what ImageJ reports about the image:
Title: FocusImage_10_exp_300_Focus T_AF_zpos_-0.139403_method_TiltUntiltFocus.tif
Width: 4302 pixels
Height: 512 pixels
Pixel size: 1x1 pixel
ID: -2
Coordinate origin: 0,0
Bits per pixel: 16 (unsigned)
Display range: 245 - 776
No Threshold
Magnification: 0.50
Uncalibrated
No Overlay
No Selection
I am looking for something similar to IrfanView on Windows for its capacity to
open a large number of formats such as the one above, and Eye of Gnome for its
simplicity. Does anybody have a good recommendation ?
Have a nice day !
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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