Importing collections of images

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If you have a loose collection of images in a directory, Endrov is still able to load them so you can save them in a proper format. Strictly speaking, this should be considered a last resort - much of the interesting data (such as resolution) has been lost and must be restored manually.

Contents

Name Based Import

Menu entry: Data -> Load namebased imageset

If your microscope stores down channel number, slice number etc into the name, then you can do a name based import. The name is specified by a string which is very similar to a printf in C or Matlab. Codes are

  • %C - Channel number
  • %F - Frame number
  • %Z - Z or slice number
  • %# - Arbitrary uninteresting number

The channel list is comma-separated (,). No additional spaces should be inserted. The first channel is 0; if you start counting on 1 then call the first channel dummy.

Example 1

If a file in channel 1, frame 4 and slice 3 is stored as foo-01-004-03.jpg then this is the string: foo-%C-%F-%Z.jpg

Example 2

Assume that you have this list of files:

DEVD_ab_Series008_z000_ch00.tif
DEVD_ab_Series008_z000_ch01.tif
DEVD_ab_Series008_z000_ch02.tif
DEVD_ab_Series008_z001_ch00.tif
DEVD_ab_Series008_z001_ch01.tif
DEVD_ab_Series008_z001_ch02.tif
DEVD_ab_Series008_z002_ch00.tif
DEVD_ab_Series008_z002_ch01.tif
DEVD_ab_Series008_z002_ch02.tif
DEVD_ab_Series008_z003_ch00.tif
DEVD_ab_Series008_z003_ch01.tif
DEVD_ab_Series008_z003_ch02.tif

The number after Series is the frame, after z is the slice, after the ch is the channel number, and each .tif-file contains a stack (gray-level). Assume that

  • Channel 0 is DIC
  • Channel 1 is GFP
  • Channel 2 is YFP

Then the pattern is DEVD_ab_Series%F_z%Z_ch%C.tif and the channels are DIC,GFP,YFP.

Example 3

Not everyone start counting from 0 as in this case:

DEVD_ab_Series008_z000_ch01.tif
DEVD_ab_Series008_z000_ch02.tif
DEVD_ab_Series008_z001_ch01.tif
DEVD_ab_Series008_z001_ch02.tif
DEVD_ab_Series008_z002_ch01.tif
DEVD_ab_Series008_z002_ch02.tif
DEVD_ab_Series008_z003_ch01.tif
DEVD_ab_Series008_z003_ch02.tif
  • Channel 1 is phase contrast
  • Channel 2 is GFP

Then the pattern is DEVD_ab_Series%F_z%Z_ch%C.tif and the channels are dummy,PC,GFP. Channel 0 will not be used so it can be called whatever, here "dummy". It is just to get the counting right.

Sequence Based Import

Menu entry: Data -> Load sequence imageset

If your microscope just dumps images and the channel, slice etc only depend on the position in the file listing (alphabetical order) then the sequence import is the tool. You have to specify the order in which images come. A slightly formal definition:

r###(A) - repeat A # times

A,B,C - First A, then B, then C and so on.

  • n# - The number of slices in the coming stacks. This is for the sake of speed; it would take a lot of time to build the image database if all stacks had to be scanned.
  • s... - a stack with all slices for a certain frame and channel. Takes additional semi-optional arguments:
  • c# - Channel number
  • i# - Number of seconds this capture is supposed to take
  • k# - If your stack contains images that should not be included, set this to something else than 1 (default. Setting it to 2 only includes every second image.
  • f# - Skip f slides in the beginning of the stack. Default: 0

Example:

r5(sc0i5)

with channels "foo"

Restoring metadata

After import should restore the metadata. Once the images are loaded, in the Data-menu for each Channel, you will find several tools e.g.

  • Setting resolution
  • Re-interpreting time and z-dimensions

You should go through all these. If you need new tools then please tell us. Once the data is fine, re-save data in a new file ("save as" in the data menu, you do not have to specify an extension).