Edit me
Step-by-step guides
- Generating a histogram of pixel intensities from each channel.
Predefined tasks
Some tasks are included in the Anchor distribution, to be easily
run from the command-line with -t taskname
.
To run a task, open a shell (e.g. Command Prompt
or Powershell
in Windows), change to a directory with images, and then:

Next, consider enabling additional outputs with the -o
options or refining your
inputs with the -i
options.
Image processing
Task Name |
Input Type |
Description |
histogram |
images |
extracts histograms of the intensity values an image. |
mean |
images |
creates a mean-intensity projection of all inputs. |
meanResize |
images |
scales inputs to fixed dimensions, and then a mean-intensity projection. |
resize |
images |
scales each image to fit inside fixed dimensions, preserving aspect ratio. Optionally accepts -pr. |
stack/montage |
images (3D) |
produces a tiled montage of all z-slices of a 3D image |
Image segmentation
Task Name |
Input Type |
Description |
text |
images |
finds text-regions in images. |
File copying / conversion
Task Name |
Input Type |
Description |
anonymize |
any files |
copies files, randomizing order and hiding the original naming. |
convert |
images |
converts the file format of input images. |
copy |
any files |
copies files, preserving naming and subdirectory structure. |
Task Name |
Input Type |
Description |
countFiles |
any files |
counts the number of input-files. |
list |
any files |
shows a line inputName -> inputPath for each input. |
listNames |
any files |
shows each input’s name on a separate line. |
listPaths |
any files |
shows each input’s path on a separate line. |
summarize |
images |
combines the summaries in summarizeImages and summarizePaths . |
summarizeImages |
images |
summarizes image attributes (dimensions, bit depth etc.) |
summarizePaths |
any files |
summarizes file attributes (size, patterns among the file-paths etc.) |