Skip to content
OpenReadout

preview

preview renders a PNG or JPEG picture of the data: an image plane, a channel composite or a maximum projection; a trace; a mass spectrum; or a plate heat map.

openreadout preview [OPTIONS] <FILE>

The kind of picture follows the file: images first, then traces, spectra and plate tables. The trace, spectrum and plate flags pick another. The same request on the same file always gives the same bytes.

Flags

Output

  • -o, --output FILE: .png or .jpg; - writes the image to stdout. Default: <input stem>.preview.png next to the input.
  • --format png|jpeg: default from the output extension, else PNG.
  • --quality N: JPEG quality, 1–100. Default 90.
  • --max-size N: longest side of the picture in pixels (16–8192), rulers included. Default 1024.
  • --overwrite: replace an existing output file.
  • --json: print the report as JSON.

Images

  • --image N: image index. Default 0.
  • --select SEL: planes, such as c=1, z=4 or c=0,1,z=2. Repeatable. Default: channel 0, the middle z, t 0. Several channels imply --composite.
  • --mip z|t: maximum-intensity projection over z or t, limited to the selected range.
  • --composite: blend all (or the selected) channels in their colours.
  • --level N: pyramid level. Default: the level nearest --max-size.
  • --region X,Y,W,H: only this rectangle, in full-resolution pixels (or in the pixels of --level when one is given).
  • --contrast auto|min-max|percentile:LO,HI|raw: auto stretches the 0.1–99.9 percentiles. Default auto.
  • --lut gray|channel-color: default gray for one channel, channel colours for composites.
  • --plain: no rulers, scale bar or frame.
  • --grid: faint grid lines at the ruler ticks.

Traces, spectra and plates

  • --trace N, --sweep N, --channel N: the trace, sweep and channels to draw (--channel is repeatable; default the first 8).
  • --run N, --spectrum N, --scan N: the mass spectrum to draw, by zero-based index or instrument scan number.
  • --centroid: draw the instrument’s centroid list instead of the profile.
  • --table N, --column NAME: the plate table, and the value column of a long layout.

NMR

  • --process: draw FIDs as spectra processed by OpenReadout.
  • --process-phase MODE, --process-lb HZ, --process-size N, --process-baseline MODE: processing settings. See analyze nmr-peaks.

Examples

Terminal window
$ openreadout preview doctor.tif -o doctor.png
wrote doctor.png (47x49 png, 203 bytes, verified=true): image 0 level 0 c=[0] z=[1] t=[0] contrast percentile:0.1,99.9
view it: open (or Read) doctor.png; zoom with --region X,Y,W,H in full-res px read off the rulers (now showing 0,0,16,8)
Terminal window
openreadout preview cells.czi --select c=0,1,2 --mip z -o cells.png
openreadout preview run.raw --scan 1200 -o scan1200.png

Zooming into large images

Image previews have rulers along the top and left edges in full-resolution pixel coordinates, whatever level was drawn. Read coordinates off the picture and pass them back as --region X,Y,W,H to zoom in. preview then reads the coarsest pyramid level that still shows the region at --max-size, so zooming into any part of a whole-slide image reads only a few tiles. The JSON report maps picture pixels back to source pixels (image.plot_area, source_origin, source_per_pixel).

JSON

preview.

Run openreadout preview --help for the full help of your installed version.