#PABI 2025 was successfully completed!
Processing and Analysis of Biological Images workshop, organized and executed by #CELLIMteam, @ceitec.eu and CBIA.
We learned about detectors, image pre-processing, FAIR data, #CellProfiler and #FIJI
#workshop #bioimageanalysis #lightmicroscopy #bioimaging
If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I
11/
We also ship a benchmark dataset of Golgi morphologies and use it to compare image featurization tools: #ConvNeXt, #SubCell, #CellProfiler
@bethcimini.bsky.social
#CellProfiler
question that I am struggling to look up on the forum:
Is there a module where I can make an image where each object is given the intensity of something I measured? (Like the 'number of neighbors' and 'percent touching' images, but e.g. cell area or whatever.)
Our first two episodes (on handling out of focus regions in images, as well as on how to download data from the IDR) are available now, with new episodes will drop ~every two weeks(ish)!
While it will heavily feature #CellProfiler, we will use whatever tool is right for the challenge. (2/x)
only took me 4 hours this time to get all dependencies sorted out to run #cellpose in #cellprofiler. Documentation is great for both, but every system I install this on has it's own set of problems to get started. sigh.
🚨 @globias.bsky.social is launching Call4Help: personalized guidance for image analysis challenges! 🌟
📅 1st session: 20–24 Jan 2025
💡 Tools: #Napari, #Ilastik, #CellProfiler
🌍 Expert-led, global time zones
🔗 Apps open 6 Jan. Share your insights:
forms.gle/SSgMXxrto2wV...
#ImageAnalysis
Becoming a convert to #CellProfiler (still a step off #Fiji/#ImageJ, but it’s making life a lot easier!!!!!)
