Locates wells in whole-plate and multi-well crystal violet plaque-assay images. The front half of a two-stage pipeline with Toxoplasma Plaque v1; the well it finds also gives the diameter that makes areas comparable across microscopes. This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Toxoplasma Plaque Well Detector v1 in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. This is a plaque-assay model and is driven by…
Open weights
mit
spacr
Segments nuclei from the host cell mask channel alone — no nuclear stain required. A cross-channel model: it is given the cell image and predicts where the nuclei are, freeing the DAPI/Hoechst channel for another marker. This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Cross-channel nuclei-from-cellmask (Cellpose-SAM) in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. Point spaCR's mask generation at the downloaded…
Open weights
mit
spacr
Segments Toxoplasma gondii plaques in crystal violet plaque assays. Round 3. Use it through spaCR's plaque module. This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Toxoplasma Plaque v1 in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. This is a plaque-assay model and is driven by spaCR's plaque module rather than In the GUI the same thing is under Make masks in the plaque workflow.…
Open weights
mit
spacr
Segments Toxoplasma gondii parasitophorous vacuoles from a parasite stain (anti-Toxoplasma-biotin, or DsRed in the PV lumen). Round 2. This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Toxoplasma PV v1 in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. Point spaCR's mask generation at the downloaded checkpoint: In the GUI the same thing is under Make masks — choose the downloaded model in the Cellpose model field for…
Open weights
mit
spacr
Segments Toxoplasma gondii parasitophorous vacuoles from a parasite stain (anti-Toxoplasma-biotin, or DsRed in the PV lumen). Round 5 — the current promoted PV model, superseding round 2 (Toxoplasma PV v1). This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Toxoplasma PV v2 (round 5) in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. Point spaCR's mask generation at the downloaded checkpoint: In the GUI the same thing…
Open weights
mit
spacr
Segments Toxoplasma gondii parasitophorous vacuoles from the host cell mask channel alone — no parasite-specific stain required. A cross-channel model: it is given the host cell image and predicts where the parasites are. This model is distributed through the spaCR Model Zoo. spaCR is an open-source package for spatial phenotype analysis of CRISPR screens and microscopy images. Launch the GUI and open the Model Zoo: Find Toxoplasma from Cell Mask (cross-channel) in the model list and press Download. The Model Zoo verifies the checkpoint's SHA-256 after download, so a truncated or substituted file is rejected rather than silently used. Point spaCR's mask generation at the downloaded…
Open weights
mit
spacr
