Distorted nd2 files

Usage & Issues
,
#1

Hi bioformats team,

has this issue already been resolved?

Nd2 files appears distorted in ImageJ

I get the same problem now when opening in FIJI, as well as when uploading to OMERO.

Or could this have to do with the version of nd2 file? in the nis elements it opens fine and sais it is version 4.30.02 with which this was made.

all information shared below

Dimensions: XY(1) x λ(1)
Camera Name: Mono Camera Nikon DS-Ri2 (emulated)
Numerical Aperture: 0.3
Refractive Index: 1
Name: Hoechst
Component Count: 1
Modality: Widefield Fluorescence
Camera Settings:
Camera Type: Nikon DS-Ri2
Binning: 3x3
Exposure: 400 ms
Gain: 47.1x
Sharpness: Medium
Brightness: 0.00
Hue: 0.00
Saturation: 0.00
WB Red: 0.77
WB Blue: 7.15
Scene Mode: Neutral
Trigger Mode: Internal
Microscope Settings: Microscope: Ti Microscope
Nikon Ti, FilterChanger(Turret1): 1 (DAPI)
Nikon Ti, Shutter(INTSL): Opened
Nikon Ti, Illuminator(Illuminator-DIA): Remote Switch On
Nikon Ti, Illuminator(Illuminator-DIA): Off
Nikon Ti, Illuminator(Illuminator-DIA) Voltage: -1.0
Nikon Ti, Illuminator(Illuminator-EPI) NDFilter: 100.0
PFS, state: On
PFS, offset: 4986
PFS, mirror: Inserted
Zoom: 1.00x

#2

Hi @Joost_Willemse1, we still have some known bugs with the nd2 format. The previous distorted images we had seen appeared to have the incorrect channel count and pixel type. Do these values look correct in the metadata when loaded in Fiji?

Also, it likely wont have an impact but it may also be worth checking that changing the below setting doesn’t make a difference:

Plugins > Bio-Formats > Bio-Formats Plugins Configuration
Go to Formats > Nikon ND2
Change the value for "Chunkmap" and try to reimport
1 Like
#3

I already tried that, no difference indeed.

The channel count (sizeC) is 1 which is true
pixeltype is uint8, dont know what it should be?

i also uploaded the file here

Joost

#4

Thanks Joost, we received the file and I was able to reproduce the issue with the latest Bio-Formats. It does indeed look to be the same issue as the one previously reported. I have updated the existing GitHub Issue to link to this thread and the new sample file: https://github.com/ome/bioformats/issues/3152

1 Like