🔬 ML-based segmentation (CellPose, ilastik, QuPath) will replace manual ImageJ counting
Why: reproducibility, throughput, objective quantitation
Lore: Reviewers now expect automated or blinded image analysis
(9/10)
Why: reproducibility, throughput, objective quantitation
Lore: Reviewers now expect automated or blinded image analysis
(9/10)
November 9, 2025 at 4:50 PM
🔬 ML-based segmentation (CellPose, ilastik, QuPath) will replace manual ImageJ counting
Why: reproducibility, throughput, objective quantitation
Lore: Reviewers now expect automated or blinded image analysis
(9/10)
Why: reproducibility, throughput, objective quantitation
Lore: Reviewers now expect automated or blinded image analysis
(9/10)
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
www.biorxiv.org
November 9, 2025 at 3:53 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
November 7, 2025 at 7:23 PM
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
www.biorxiv.org
November 6, 2025 at 3:46 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
Anyone know if any good apps for estimating surface area? (Or maybe manual/imageJ are the best alternatives?)
We're measuring surface area of bird wings tomorrow with grid paper but I'm hoping to improve the class in the future!
We're measuring surface area of bird wings tomorrow with grid paper but I'm hoping to improve the class in the future!
November 5, 2025 at 6:33 PM
Anyone know if any good apps for estimating surface area? (Or maybe manual/imageJ are the best alternatives?)
We're measuring surface area of bird wings tomorrow with grid paper but I'm hoping to improve the class in the future!
We're measuring surface area of bird wings tomorrow with grid paper but I'm hoping to improve the class in the future!
For the first demand I think the magic montage could more adapted, I prefer to keep everything as simple as possible, and for the second you can try the ''montage to stack'' ImageJ command 😁
November 5, 2025 at 4:22 PM
For the first demand I think the magic montage could more adapted, I prefer to keep everything as simple as possible, and for the second you can try the ''montage to stack'' ImageJ command 😁
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
November 5, 2025 at 3:44 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
www.biorxiv.org
November 5, 2025 at 3:44 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
www.biorxiv.org
November 5, 2025 at 3:44 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
www.biorxiv.org
November 5, 2025 at 3:44 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #RRID
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
November 5, 2025 at 3:44 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
November 4, 2025 at 10:40 PM
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
Thanks for doing this! In the wake of the loss of functioning Clear volume in FIJI/ImageJ, I went through a similar process. It is a *GREAT* platform but takes more effort to get started (and render the figures you want) than the easy/WYSIWYG of the ClearVolume GUI.
November 4, 2025 at 12:52 PM
Thanks for doing this! In the wake of the loss of functioning Clear volume in FIJI/ImageJ, I went through a similar process. It is a *GREAT* platform but takes more effort to get started (and render the figures you want) than the easy/WYSIWYG of the ClearVolume GUI.
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
www.biorxiv.org
November 3, 2025 at 3:40 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
November 2, 2025 at 3:37 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
www.biorxiv.org
November 2, 2025 at 3:37 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
And thanks to @joachimgoedhart.bsky.social for the Bouncy-Curtain imageJ plugin.
github.com/JoachimGoedh...
github.com/JoachimGoedh...
GitHub - JoachimGoedhart/Bouncy-Curtain: ImageJ/FIJI macro to generate an animated, curtain-style comparison of two images
ImageJ/FIJI macro to generate an animated, curtain-style comparison of two images - JoachimGoedhart/Bouncy-Curtain
github.com
October 29, 2025 at 9:44 AM
And thanks to @joachimgoedhart.bsky.social for the Bouncy-Curtain imageJ plugin.
github.com/JoachimGoedh...
github.com/JoachimGoedh...
imageJ does that no?
October 28, 2025 at 5:00 PM
imageJ does that no?
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
www.biorxiv.org
October 27, 2025 at 2:24 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
ImageJ should be able to open them and save into other formats (and show them in different lookup tables too).
October 27, 2025 at 2:04 PM
ImageJ should be able to open them and save into other formats (and show them in different lookup tables too).
There's a caveat - ImageJ assumes that slice positions are regularly spaced throughout the volume and doesn't check if slices' declared real positions differ from the assigned image location based on their order on a regular pixel grid.
October 27, 2025 at 12:53 PM
There's a caveat - ImageJ assumes that slice positions are regularly spaced throughout the volume and doesn't check if slices' declared real positions differ from the assigned image location based on their order on a regular pixel grid.
ImageJ/Fiji users will be pleased to know that opening a DICOM stack with File > Import > Image Sequence results in correctly calibrated z pixel spacing.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
October 27, 2025 at 11:08 AM
ImageJ/Fiji users will be pleased to know that opening a DICOM stack with File > Import > Image Sequence results in correctly calibrated z pixel spacing.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
www.biorxiv.org
October 26, 2025 at 2:22 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
www.biorxiv.org
October 25, 2025 at 2:19 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
www.biorxiv.org
October 25, 2025 at 2:19 PM
Authors published a paper in Biorxiv, they used ImageJ in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #RRID