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CHANGELOG.md

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Changelog for nd2tool

0.1.8

  • Bug fix, avoids crashing if the metadata for the objective is missing. This happened in an image from a microscope with a broken objective turret.

    After the fix, this is what nd2tool reports:

    nd2tool iiJPC526_20240828_001.nd2 --info
Warning: Could not find channel/microscope/immersionRefractiveIndex
Warning: Could not find channel/microscope/objectiveNumericalAperture
5 FOV in 3 channels:
   #1 'a594', λ_em=590.0 #FFB300
   #2 ' tmr', λ_em=542.0 #00FF00
   #3 'dapi', λ_em=432.0 #9900FF
Bits per pixel: 16, significant: 16
dx=1000.0 nm, dy=1000.0 nm, dz=300.0 nm
NA=0.000, ni=0.000
Objective Name: Uncalibrated
Objective Magnification: 1.0X
Volume size: 1024 x 1024 x 41
Looping: Dimensions: XY(5) x λ(3) x Z(41)
Camera: Andor DU-888 X-9877

    If it wasn't obvious that the information was wrong here, we could make a special case when the objective name is set to Uncalibrated.

    In that case it does not make sense to report these values (found in the metadata!)

    Objective Magnification: 1.0X
dx=1000.0 nm, dy=1000.0 nm

    Furthermore we should also prevent nd2tool from reporting these default values:

    NA=0.000, ni=0.000

0.1.7

  • Updating to Nikon libraries v 1.7.6.
  • Total switch to cmake for building and package creation.

0.1.6

  • Parsing Camera name and Microscope name from the text section of the metadata. This part of the metadata isn't very well structured so I wouldn't be surprised if it doesn't work for all files. If it doesn't work no info will be printed and that's all.

0.1.5

  • Added checks for some unlikely scenarios. Builds cleanly with clang, i.e., with scan-build make -B CC=clang DEBUG=1 as well as gcc make -B DEBUG=1.
  • Added the --SpaceTx option to save one image per plane according to the SpaceTx convention. This closes [#4]. Please note that for fov_id the name of the nd2 file is used (which can contain underscores) and 0 is used for round_label. In other words, you might need to rename the files (for example with rename in linux) before processing them with starfish.

0.1.4

  • Added the --dry option for dry runs which tells the program not to create or modify any folders or files.
  • Added the --deconwolf option to generate a script with commands to run deconwolf on the tif files (unless converted with the --composite flag).
  • Factored out some code into nd2tool_util.c

0.1.3

  • Experimental support for writing composite images with the --composite flag. It remains to choose color maps that makes sense.

0.1.2

  • Added the --coord command line option that will print the position of all images in csv format to the standard output. To be validated together with --shake.

0.1.1

  • Experimental (still to be validated and hence not enabled by default) shake detection in the axial direction, enable with the --shake command line argument.

0.1.0

  • Slightly improved log file messages.

0.0.6

  • Fixed problem with non quadratic image sizes.
  • Not saying when it is using the BigTIFF format any more.

0.0.5

  • added approximate conversion from emission wavelength to color.