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Populate "BF Channel" list with presets containing keywords #287

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merged 6 commits into from
Nov 29, 2022
Merged

Populate "BF Channel" list with presets containing keywords #287

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69c29b8
Populate if preset name contain any of a list of keywords
talonchandler Nov 24, 2022
52e9b04
Better keywords; insensitive to case
talonchandler Nov 24, 2022
57be9d1
Better comment
talonchandler Nov 24, 2022
d893c56
Typos
talonchandler Nov 24, 2022
0238225
docs
talonchandler Nov 24, 2022
f0f7791
Add "phase" and "ph" as keywords
talonchandler Nov 29, 2022
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10 changes: 9 additions & 1 deletion docs/microscope-installation-guide.md
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Original file line number Diff line number Diff line change
Expand Up @@ -54,9 +54,17 @@ Add 5 presets to this group named `State0`, `State1`, `State2`, `State3`, and `S

![](https://github.com/mehta-lab/recOrder/blob/main/docs/images/create_preset.png)

### (Optional) Enable "Phase From BF" acquisition

If you would like to reconstruct phase from brightfield, add a `Micromanager` preset with brightfield properties (e.g. moving the polarization analyzer out the light path) and give the preset a name that contains one of the following case-insensitive keywords:

`["bf", "brightfield", "bright", "labelfree", "label-free", "lf", "label"]`

In `recOrder` you can select this preset using the `Acquisition Settings > BF Channel` dropdown menu.

### Enable port access

Finally, enable port access so that micromanager can communicate with recOrder through the `pycromanager` bridge. To do so open MM and navigate to `Tools > Options` and check the box that says `Run server on port 4827`
Finally, enable port access so that `Micromanager` can communicate with recOrder through the `pycromanager` bridge. To do so open `Micromanager` and navigate to `Tools > Options` and check the box that says `Run server on port 4827`

![](https://github.com/mehta-lab/recOrder/blob/main/docs/images/run_port.png)

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8 changes: 5 additions & 3 deletions recOrder/plugin/main_widget.py
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Expand Up @@ -896,11 +896,13 @@ def connect_to_mm(self):
)
config_group_found = True
self.ui.cb_config_group.addItem(group)
# not entirely sure what this part does, but I left it in
# I think it tried to find a channel such as 'BF'

# Populate the acquisition "BF channel" list with presets that contain any of these keywords
bf_keywords = ["bf", "brightfield", "bright", "labelfree", "label-free", "lf", "label"]
for ch in config_list:
if ch not in self.calib_channels:
if any([keyword.lower() in ch.lower() for keyword in bf_keywords]):
self.ui.cb_acq_channel.addItem(ch)

if not config_group_found:
msg = (
f"No config group contains channels {self.calib_channels}. "
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