# Latest **URL:** https://forum.image.sc/latest.md [Latest](https://forum.image.sc/latest.md) · [Categories](https://forum.image.sc/categories.md) · [Tags](https://forum.image.sc/tags.md) --- ## [Guidelines](https://forum.image.sc/t/guidelines/5)
**Author:** [@system](https://forum.image.sc/u/system)\ **Replies:** 1\ **Last updated:** [September 17, 2015, 3:11pm UTC](https://forum.image.sc/t/guidelines/5 "2015-09-17T15:11:30Z")
This is a Civilized Place for Public Discussion Please treat this discussion forum with the same respect you would a public park. We, too, are a shared community resource — a place to share skills, knowledge and inter… --- ## [Related Communities](https://forum.image.sc/t/related-communities/33872)
**Author:** [@ctrueden](https://forum.image.sc/u/ctrueden)\ **Replies:** 0\ **Last updated:** [February 10, 2020, 7:57pm UTC](https://forum.image.sc/t/related-communities/33872 "2020-02-10T19:57:28Z")
There are several other community forums whose topics overlap with this one: Microforum’s focus is hardware, acquisition, and specimen-related aspects of scientific imaging, particularly (but not limited to) theory a… --- ## [Welcome to the Image.sc Forum!](https://forum.image.sc/t/welcome-to-the-image-sc-forum/18727)
**Author:** [@ctrueden](https://forum.image.sc/u/ctrueden)\ **Replies:** 0\ **Last updated:** [August 2, 2018, 5:55pm UTC](https://forum.image.sc/t/welcome-to-the-image-sc-forum/18727 "2018-08-02T17:55:33Z")
Welcome to the Scientific Community Image Forum at forum.image.sc! This forum’s focus is software-oriented aspects of scientific imaging, particularly (but not limited to) image analysis, processing, acquisition, storag… --- ## [Quantification of nuclei](https://forum.image.sc/t/quantification-of-nuclei/122677)
**Author:** [@Malvina](https://forum.image.sc/u/Malvina)\ **Replies:** 10\ **Last updated:** [October 6, 2026, 10:42am UTC](https://forum.image.sc/t/quantification-of-nuclei/122677 "2026-10-06T10:42:52Z")
Hello, I need your help, please. :folded\_hands: I'd like to count the number of nuclei in this image so that I can then count the number of positive nuclei labeled with another antibody. I’ve already tried Trainable W… --- ## [If 3D viewer is used Fiji crashes](https://forum.image.sc/t/if-3d-viewer-is-used-fiji-crashes/116669)
**Author:** [@zoe7](https://forum.image.sc/u/zoe7)\ **Replies:** 10\ **Last updated:** [October 6, 2026, 10:39am UTC](https://forum.image.sc/t/if-3d-viewer-is-used-fiji-crashes/116669 "2026-10-06T10:39:59Z")
I have a z stack of micro CT images and i would like to make a 3D image. I watched this yt video “How to use Fiji or ImageJ to create a 3D image using 3D viewer plugin”. However, once i clicked on the 3D viewer my Fiji c… --- ## [SAMJ - 'libmamba' problem installing models](https://forum.image.sc/t/samj-libmamba-problem-installing-models/122741)
**Author:** [@Volko](https://forum.image.sc/u/Volko)\ **Replies:** 0\ **Last updated:** [October 6, 2026, 8:37am UTC](https://forum.image.sc/t/samj-libmamba-problem-installing-models/122741 "2026-10-06T08:37:02Z")
Hi, I just installed the SAMJ plugin to try it out, but run into a problem when trying to install any of the models. The model installation appears to start appropriately, but after a short while the process is terminat… --- ## [Cell Length X measurements](https://forum.image.sc/t/cell-length-x-measurements/122683)
**Author:** [@stv](https://forum.image.sc/u/stv)\ **Replies:** 1\ **Last updated:** [October 6, 2026, 1:35am UTC](https://forum.image.sc/t/cell-length-x-measurements/122683 "2026-10-06T01:35:56Z")
Hello, Is there somebody able to explain me how the Cell Length X measurement is calculated? I thought that it was a simple subtraction between maximal and minimal x coordinates of the 3D cell, but the results I obtaine… --- ## [Are my cells NeuN+?](https://forum.image.sc/t/are-my-cells-neun/122691)
**Author:** [@repnovis1992](https://forum.image.sc/u/repnovis1992)\ **Replies:** 3\ **Last updated:** [October 6, 2026, 1:18am UTC](https://forum.image.sc/t/are-my-cells-neun/122691 "2026-10-06T01:18:34Z")
Background :bulb: Hello, I'm a master's student with a project in reprogramming glial cells into neurons using pro-neuronal transcription factors. I am responsible for making classifiers and quantifying the visual data i… --- ## [Issues getting Trackmate-CellposeSAM to work, even when cellpose in Python works or when cellpose in Fiji works](https://forum.image.sc/t/issues-getting-trackmate-cellposesam-to-work-even-when-cellpose-in-python-works-or-when-cellpose-in-fiji-works/122317)
**Author:** [@ErinMRichards](https://forum.image.sc/u/ErinMRichards)\ **Replies:** 6\ **Last updated:** [October 5, 2026, 11:43pm UTC](https://forum.image.sc/t/issues-getting-trackmate-cellposesam-to-work-even-when-cellpose-in-python-works-or-when-cellpose-in-fiji-works/122317 "2026-10-05T23:43:04Z")
Hi all! I've been having issues implementing Trackmate-Cellpose in ImageJ/Fiji. I always get "Found 0 spots." when clicking Preview while using the Cellpose-SAM detector in Trackmate-Cellpose. Computer setup info: Wi… --- ## [JPEG XL for Fiji: lossless hyperstacks 15–51 % smaller than TIFF (update site "Panamage")](https://forum.image.sc/t/jpeg-xl-for-fiji-lossless-hyperstacks-15-51-smaller-than-tiff-update-site-panamage/122738)
**Author:** [@stefan.zobel](https://forum.image.sc/u/stefan.zobel)\ **Replies:** 0\ **Last updated:** [October 5, 2026, 9:38pm UTC](https://forum.image.sc/t/jpeg-xl-for-fiji-lossless-hyperstacks-15-51-smaller-than-tiff-update-site-panamage/122738 "2026-10-05T21:38:22Z")
Hi all, I'd like to announce a Fiji plugin that opens and saves JPEG XL (.jxl) files. It is part of panamage ( GitHub - stefan-zobel/panamage: JPEG XL for Java 21+ via libjxl and Panama (FFM API): decode, encode, lossle… --- ## [Transfer a specific annotation through warpy](https://forum.image.sc/t/transfer-a-specific-annotation-through-warpy/122737)
**Author:** [@toadflesh](https://forum.image.sc/u/toadflesh)\ **Replies:** 0\ **Last updated:** [October 5, 2026, 9:15pm UTC](https://forum.image.sc/t/transfer-a-specific-annotation-through-warpy/122737 "2026-10-05T21:15:48Z")
Hey guys! So I have gotten the hang of using warpy in qupath more or less and I was wondering if there is a way to transfer only one annotation to another image? Since the default script is for the whole list of annotat… --- ## [How to improve the accuracy of a pipeline counting live and dead yeast cells?](https://forum.image.sc/t/how-to-improve-the-accuracy-of-a-pipeline-counting-live-and-dead-yeast-cells/122696)
**Author:** [@MonsteraB](https://forum.image.sc/u/MonsteraB)\ **Replies:** 5\ **Last updated:** [October 5, 2026, 9:10pm UTC](https://forum.image.sc/t/how-to-improve-the-accuracy-of-a-pipeline-counting-live-and-dead-yeast-cells/122696 "2026-10-05T21:10:36Z")
This image is an example of the pipeline output with manual counts on top: The pipeline determines the grid (teal border) and within it, circles live cells in green and dead cells in red. The green and red dots on top… --- ## [Requests for creating ImageJ update sites](https://forum.image.sc/t/requests-for-creating-imagej-update-sites/40051)
**Author:** [@frauzufall](https://forum.image.sc/u/frauzufall)\ **Replies:** 645\ **Last updated:** [October 5, 2026, 7:54pm UTC](https://forum.image.sc/t/requests-for-creating-imagej-update-sites/40051 "2026-10-05T19:54:59Z")
Hi all, since imagej.net is still down and since it will change it’s nature from mediawiki to github pages, the mechanism to create update sites by creating a wiki user cannot be applied anymore. All existing update si… --- ## [Measuring Thickness, Curviness, Length, and Orientation of Individual Fibers in ilastik](https://forum.image.sc/t/measuring-thickness-curviness-length-and-orientation-of-individual-fibers-in-ilastik/122733)
**Author:** [@Acer\_Chafee](https://forum.image.sc/u/Acer_Chafee)\ **Replies:** 1\ **Last updated:** [October 5, 2026, 6:22pm UTC](https://forum.image.sc/t/measuring-thickness-curviness-length-and-orientation-of-individual-fibers-in-ilastik/122733 "2026-10-05T18:22:50Z")
Hi everyone, I’m using ilastik to detect individual fibers in microscopy images, and I’m trying to measure the following for each detected fiber: Thickness Curviness/tortuosity Length Orientation I’ve see… --- ## [Research engineer in Bioimage Analysis. Institut Pasteur, Image Analysis Hub - 2026](https://forum.image.sc/t/research-engineer-in-bioimage-analysis-institut-pasteur-image-analysis-hub-2026/122732)
**Author:** [@tinevez](https://forum.image.sc/u/tinevez)\ **Replies:** 0\ **Last updated:** [October 5, 2026, 3:58pm UTC](https://forum.image.sc/t/research-engineer-in-bioimage-analysis-institut-pasteur-image-analysis-hub-2026/122732 "2026-10-05T15:58:31Z")
Dear all Below is an announcement for a permanent position as a Research Engineer in the Institut Pasteur, Paris. We are looking ideally for a Bioimage Analyst to support the services and projects of the core facili… --- ## [UK-BIAS online helpdesk and introduction](https://forum.image.sc/t/uk-bias-online-helpdesk-and-introduction/122731)
**Author:** [@Marie-nkaefer](https://forum.image.sc/u/Marie-nkaefer)\ **Replies:** 0\ **Last updated:** [October 5, 2026, 3:08pm UTC](https://forum.image.sc/t/uk-bias-online-helpdesk-and-introduction/122731 "2026-10-05T15:08:22Z")
We are pleased to announce the first virtual helpdesk from UK-BIAS – the dedicated bioimage analysis service in the UK Node of Euro-BioImaging (flyer attached).This will take place on Tuesday 10 November, 14.00-15.30 GMT.… --- ## [Add enhance contrast hotkey \[e\] to vanilla Fiji](https://forum.image.sc/t/add-enhance-contrast-hotkey-e-to-vanilla-fiji/122688)
**Author:** [@Christian\_Tischer](https://forum.image.sc/u/Christian_Tischer)\ **Replies:** 12\ **Last updated:** [October 5, 2026, 2:53pm UTC](https://forum.image.sc/t/add-enhance-contrast-hotkey-e-to-vanilla-fiji/122688 "2026-10-05T14:53:41Z")
Hi all, during an ImageJ macro course today, I learned that a colleague has added this to the startup macros of ImageJ: macro "Enhance Contrast \[e\]" { run("Enhance Contrast", "saturated=0.35"); } to me, this is a gam… --- ## [\[QuPath 0.6.0rc1\] Unable to read remote OME-Zarr by URL](https://forum.image.sc/t/qupath-0-6-0rc1-unable-to-read-remote-ome-zarr-by-url/101605)
**Author:** [@psobolewskiPhD](https://forum.image.sc/u/psobolewskiPhD)\ **Replies:** 44\ **Last updated:** [October 5, 2026, 2:38pm UTC](https://forum.image.sc/t/qupath-0-6-0rc1-unable-to-read-remote-ome-zarr-by-url/101605 "2026-10-05T14:38:59Z")
Really excited by the prospects of ome-zarr in QuPath! We’ve been doing some testing and it appears that local ome-zarr work just fine, which is great, but I’ve been unable to read a remote OME-zarr. (Note: I unchecked… --- ## [ImSwitch2 Announcement: Beta Version Online](https://forum.image.sc/t/imswitch2-announcement-beta-version-online/122729)
**Author:** [@Lenny](https://forum.image.sc/u/Lenny)\ **Replies:** 0\ **Last updated:** [October 5, 2026, 1:50pm UTC](https://forum.image.sc/t/imswitch2-announcement-beta-version-online/122729 "2026-10-05T13:50:00Z")
Hi everyone, We, that is Guillaume Minet, Karl Höjlund and me Lenny Reinkensmeier from the Testa lab at SciLifeLab, Stockholm spent the last months rebuilding and extending ImSwitch for the microscopes we run every day,… --- ## [Spatial analysis of RNAscope](https://forum.image.sc/t/spatial-analysis-of-rnascope/122710)
**Author:** [@Mko](https://forum.image.sc/u/Mko)\ **Replies:** 8\ **Last updated:** [October 5, 2026, 1:47pm UTC](https://forum.image.sc/t/spatial-analysis-of-rnascope/122710 "2026-10-05T13:47:38Z")
Hello, I have a RNAscope experiment where I'm checking the expression of 3 different markers on mouse colon tissue in the epithelium. I have segmented the cells with instanseg(dapi+epcam) and I have used subcellular de… --- ## [Quantitating Image analysis](https://forum.image.sc/t/quantitating-image-analysis/122701)
**Author:** [@hamzat\_toheeb](https://forum.image.sc/u/hamzat_toheeb)\ **Replies:** 4\ **Last updated:** [October 5, 2026, 1:10pm UTC](https://forum.image.sc/t/quantitating-image-analysis/122701 "2026-10-05T13:10:21Z")
Hello, I am new here and would like to seek your guidance. I'm currently working on biofilm research and require assistance with image quantification using BiofilmQ software. My Image is in 2D format, as it was extracted… --- ## [A new home for the OME-zarr Python stack](https://forum.image.sc/t/a-new-home-for-the-ome-zarr-python-stack/122698)
**Author:** [@JohannesSoltwedel](https://forum.image.sc/u/JohannesSoltwedel)\ **Replies:** 2\ **Last updated:** [October 5, 2026, 12:45pm UTC](https://forum.image.sc/t/a-new-home-for-the-ome-zarr-python-stack/122698 "2026-10-05T12:45:38Z")
A new home for the OME-Zarr Python stack In the past year or so, a lot of development has happened on ome-zarr-py, napari-ome-zarr and ome-zarr-models-py. Our current efforts revolve a lot around cleanly separating conce… --- ## [Open Bioimaging Practices Meetups: Fall 2026 program](https://forum.image.sc/t/open-bioimaging-practices-meetups-fall-2026-program/122564)
**Author:** [@jluethi](https://forum.image.sc/u/jluethi)\ **Replies:** 2\ **Last updated:** [October 5, 2026, 11:38am UTC](https://forum.image.sc/t/open-bioimaging-practices-meetups-fall-2026-program/122564 "2026-10-05T11:38:21Z")
I'm happy to announce the fall 2026 Open Bioimaging Practices Meetup schedule. We'll have 3 exciting meetings about developments in the OME-Zarr space: 2026-09-30T14:00:00Z (UTC) OME-Zarr viewers, part 2 ("The FIJI str… --- ## [TrackMate Batcher won't start](https://forum.image.sc/t/trackmate-batcher-wont-start/122723)
**Author:** [@HannaG](https://forum.image.sc/u/HannaG)\ **Replies:** 2\ **Last updated:** [October 5, 2026, 9:14am UTC](https://forum.image.sc/t/trackmate-batcher-wont-start/122723 "2026-10-05T09:14:10Z")
Hi Community, I need some help solving my issue that the TrackMate Batcher is not starting. I'm getting the following error: (Fiji Is Just) ImageJ 2.16.0/1.54p; Java 1.8.0\_452 \[64-bit\]; Windows 11 10.0; 387MB of 23552M… --- ## [Snapshots instead of WSI for Ki-67 analysis in neuroendocrine tumours](https://forum.image.sc/t/snapshots-instead-of-wsi-for-ki-67-analysis-in-neuroendocrine-tumours/122713)
**Author:** [@lsemkin](https://forum.image.sc/u/lsemkin)\ **Replies:** 5\ **Last updated:** [October 5, 2026, 7:45am UTC](https://forum.image.sc/t/snapshots-instead-of-wsi-for-ki-67-analysis-in-neuroendocrine-tumours/122713 "2026-10-05T07:45:25Z")
Does anyone use snapshots rather than whole-slide images (WSI) for Ki-67 assessment in QuPath? I am trying to develop a QuPath workflow to assist with Ki-67 quantification in gastric neuroendocrine tumours. Our digital … --- ## [Issue with 3d soma creation using SNT plugin](https://forum.image.sc/t/issue-with-3d-soma-creation-using-snt-plugin/122718)
**Author:** [@M1kamonst3r](https://forum.image.sc/u/M1kamonst3r)\ **Replies:** 0\ **Last updated:** [October 4, 2026, 5:49pm UTC](https://forum.image.sc/t/issue-with-3d-soma-creation-using-snt-plugin/122718 "2026-10-04T17:49:24Z")
Hi! I’ve been trying to reconstruct a neuron (file loaded using BioFormats as an .nd2) in SNT — I can do the dendrites no problem, but does anyone have any advice on how to reconstruct the soma in 3d instead of it being… --- ## [PaperFig for Illustrator: a CEP panel for scientific figure bitmaps](https://forum.image.sc/t/paperfig-for-illustrator-a-cep-panel-for-scientific-figure-bitmaps/122716)
**Author:** [@leelieber](https://forum.image.sc/u/leelieber)\ **Replies:** 0\ **Last updated:** [October 4, 2026, 3:41pm UTC](https://forum.image.sc/t/paperfig-for-illustrator-a-cep-panel-for-scientific-figure-bitmaps/122716 "2026-10-04T15:41:23Z")
Most figure work ends in Illustrator, but the bitmap still has to be prepared somewhere else. PaperFig is a free GPL-3.0 panel that does that step on the placed image. It writes an 8-bit display file for layout and leave… --- ## [SlideIO 2.10.0 and a new desktop viewer](https://forum.image.sc/t/slideio-2-10-0-and-a-new-desktop-viewer/122712)
**Author:** [@Stanislav\_Melnikov](https://forum.image.sc/u/Stanislav_Melnikov)\ **Replies:** 0\ **Last updated:** [October 4, 2026, 1:18pm UTC](https://forum.image.sc/t/slideio-2-10-0-and-a-new-desktop-viewer/122712 "2026-10-04T13:18:25Z")
Hello everyone, We have released SlideIO 2.10.0, along with the first release of SlideIO Viewer, a desktop application for looking at slides without writing any code. For anyone meeting the project for the first time: … --- ## [Interactive Offline Tutorials in Fiji](https://forum.image.sc/t/interactive-offline-tutorials-in-fiji/122704)
**Author:** [@tferr](https://forum.image.sc/u/tferr)\ **Replies:** 0\ **Last updated:** [October 3, 2026, 4:16am UTC](https://forum.image.sc/t/interactive-offline-tutorials-in-fiji/122704 "2026-10-03T04:16:20Z")
At the recent i2k2026 / bina meeting I demoed SNT, and most of the praise went to its interactive tutorials :laughing:. Several people asked whether the same approach could work for other Fiji plugins and ImageJ itself. … --- ## [CD31 blood vessel quantification in QuPath: Pixel classifier, object creation, and vessel counting](https://forum.image.sc/t/cd31-blood-vessel-quantification-in-qupath-pixel-classifier-object-creation-and-vessel-counting/122655)
**Author:** [@ztiine](https://forum.image.sc/u/ztiine)\ **Replies:** 5\ **Last updated:** [October 3, 2026, 12:14am UTC](https://forum.image.sc/t/cd31-blood-vessel-quantification-in-qupath-pixel-classifier-object-creation-and-vessel-counting/122655 "2026-10-03T00:14:49Z")
Helloo! I have created a pixel classifier in QuPath to identify blood vessels in murine tumors stained with CD31 DAB. Visually, it seems to perform quite well. My current settings are: Classifier: RTrees Resolutio… [Next page](https://forum.image.sc/latest.md?page=1)