Image metadata

Images acquired with an ACQUIFER Imaging Machine hold the acquisition metadata in the filename.

The metadata can thus be extracted by parsing the filename.

For Fiji, metadata-parsing functions are provided for the ImageJ macro-language (see example macro) and other scripting languages (see example script) upon activation of the ACQUIFER update site (request access).

For other java-based software (ICY, QuPath…), the acquifer-core java package provides this functionality.

Below is an example filename for the IM04 and the corresponding metadata values.


PO : the sub-POsition within a well, (>1 if you imaged multiple subsites within a well)

LO : “LOOP” iteration, for time-lapse acquisition, this is the timepoint index (here 2nd timepoint of the timelapse)

CO : “COLOR” this is the index of the channel, ranging from 1 to 6 (corresponding to the utilized channel)

SL : “SLICE” index of the Z-slice when imaging a stack (here 5th slice of the stack)

PX : “PiXel” the pixel size – divide this value by 10 000 for um, or divide by 10 for nm (here, 1 pixel = 3.25 µm)

PW : “Power” Relative illumination power in % (here 80%)

IN : “Integration time” – the exposure time in ms (here 20%)

TM : “TeMperature” within the sample chamber at the time of acquisition – divide by 10 to obtain the temperature in degree C° (here 28.1 °C)

: X-position of the objective in µm (or divide by 1000 for mm, here X=14.58 mm)

: Y-position of the objective in µm (or divide by 1000 for mm, here Y=11.262 mm)

Z  : Z-position of the objective. Divide this value by 10 for µm or 10 000 for mm. (here Z=21.071 mm)

: unique Timestamp in milliseconds since start of experiment

WE : “Well”, acquisition order of the well. Wells are acquired following a “snake-pattern”, therefore B12 above is imaged after A12 and has thus the index 13.