Eduardo Gonzalez Solares
--- a/stpt_pipeline/main.py
+++ b/stpt_pipeline/main.py

    if "tiff" in recipes:
        mos.to_tiff(basedir)
+
+    mos_dis = basedir / "mos.zarr"
--- a/stpt_pipeline/bead_model.py 0 → 100644
+++ b/stpt_pipeline/bead_model.py 0 → 100644
+import numpy as np
+from scipy.special import factorial
+#
+# Bead fitting procedures
+#
+
+
+def print_theta(theta):
--- a/stpt_pipeline/bead_model.py 0 → 100644
+++ b/stpt_pipeline/bead_model.py 0 → 100644
+        return np.inf
+    if y0 < -10:
+        return np.inf
+    if c < 1:
+        return np.inf
+    if s < 0.0:
+        return np.inf
+    if p < 0.0:
+        return np.inf
+    # model=1.+bead_profile_2d(xx,yy,x0,y0,rt,p,a,c)
+    model = 1. + bead_profile_supergaussian(xx, yy, x0, y0, p, s, c)
+    ll = -model + (1. + zz) * np.log(model)
+    if do_full:
+        ll -= np.log(factorial(1. + zz))
+    #
+    if do_print:
--- a/stpt_pipeline/bead_model.py 0 → 100644
+++ b/stpt_pipeline/bead_model.py 0 → 100644
+        return np.inf
+    if y0 < -10:
+        return np.inf
+    if c < 1:
+        return np.inf
+    if s < 0.0:
+        return np.inf
+    if p < 0.0:
+        return np.inf
+    # model=1.+bead_profile_2d(xx,yy,x0,y0,rt,p,a,c)
+    model = 1. + bead_profile_supergaussian(xx, yy, x0, y0, p, s, c)
+    ll = (-model + (1. + zz) * np.log(model)) * conf
+    if do_full:
+        ll -= np.log(factorial(1. + zz))
+    #
+    if do_print: