D-CryptO: deep learning-based analysis of colon organoid morphology from brightfield images
Bibliographic record
Abstract
Stem cell-derived organoids are a promising tool to model native human tissues as they resemble human organs functionally and structurally compared to traditional monolayer cell-based assays. For instance, colon organoids can spontaneously develop crypt-like structures similar to those found in the native colon. While analyzing the structural development of organoids can be a valuable readout, using traditional image analysis tools makes it challenging because of the heterogeneities and the abstract nature of organoid morphologies. To address this limitation, we developed and validated a deep learning-based image analysis tool, named D-CryptO, for the classification of organoid morphology. D-CryptO can automatically assess the crypt formation and opacity of colorectal organoids from brightfield images to determine the extent of organoid structural maturity. To validate this tool, changes in organoid morphology were analyzed during organoid passaging and short-term forskolin stimulation. To further demonstrate the potential of D-CryptO for drug testing, organoid structures were analyzed following treatments with a panel of chemotherapeutic drugs. With D-CryptO, subtle variations in how colon organoids responded to the different chemotherapeutic drugs were detected, which suggest potentially distinct mechanisms of action. This tool could be expanded to other organoid types, like intestinal organoids, to facilitate 3D tissue morphological analysis.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.015 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".