Data Interpretation

Data Interpretation

The output format varies depending on how the acquisition is performed:

Normal Acquisition

Normal acquisition refers to taking images without using any advanced features (e.g. light program). Normally each normal acquisition generates 8 files:
  1. .locb: a binary representation of the localization data.
  2. .nimb: propriatary instrument data to ONI.
  3. .tif: the raw images, either the full camera chip or a stitch of the two channels.
  4. acq.nim: the acquisition metafile.
  5. camcal.nim: the camera metafile.
  6. map.nim: the channel mapping data.
  7. thumbnail.png: a thumbnail of the localization data.
  8. locImage.tif: a rendering of the localization data. This file will be generated if the option Save A Rendered Image Of Localizations is checked in Settings > User Settings.
The result from a normal acquisition contains two channels when read in NimOS:
  1. Channel 0/Channel 1: the raw data (i.e. the wide-field images), in which Channel 0 corresponds to the left channel and Channel 1 corresponds to the right channel.
  2. G0 - Left/G0 - Right: the localization data, in which G0 - Left corresponds to the left channel and G0 - Right corresponds to the right channel.
For example, for Alexa 647, you should expect to see the raw data in Channel 1 and the localization data in G0 - Right.

Light Program Acquisition

Light program acquisition refers to taking images using the light program. Similar to a normal acquisition, normally each light program acquisition generates 8 files.
The result from a light program acquisition contains several channels depending on the program when read in NimOS:
For example, for standard ONI 3-color EV imaging (CF 488A, CF 568, and CF 647) with a 640-split system, you should expect to see:
  1. The raw data of CF 647 in Channel 1 and the corresponding localization data in G0 - Right.
  2. The raw data of CF 568 in Channel 2 and the corresponding localization data in G0 - Left.
  3. The raw data of CF 488A in Channel 4 and the corresponding localization data in G1 - Left.
The interpretation differs for a 560-split system and for detailed instructions, check here.

Multi-Acquisition

Multi-acquisition refers to taking images using the multi-acquisition program. Similar to a normal acquisition, normally each multi-acquisition generates 8 files per laser/position/timepoint. If Combine Datasets is checked, additional files will be generated, in which the two channels are combined into a Hyperstack.
The result from a multi-acquisition contains two channels per laser/position/timepoint when read in NimOS.

Confocal Acquisition

Confocal acquisition refers to taking images with confocal enabled. Besides the 7 files generated from a normal acquisition (without the ".locb" file), normally each confocal acquisition generates additional 5 files:

  1. confocal.tif: the confocal image of each channel.
  2. widefield.tif: the wide-field image of each channel.
  3. scparams.nim: the confocal processing data.
Similar to a normal acquisition, the result from a confocal acquisition contains two channels when read in NimOS, however, both G0 - Left and G0 - Right are "empty". Click on Run Localization to run localization.

3D Acquisition

3D acquisition refers to taking images with the 3D lens engaged. Similar to a normal acquisition, normally each 3D acquisition generates 8 files, in which the Z positions are encoded in the ".locb" file.
Similar to a normal acquisition, the result from a 3D acquisition contains two channels when read in NimOS. However, the filter function will contain filtering options for the Z axis:
If at any point you are having issues with the interpretation process, please do not hesitate to contact the CX team.